Starting phenix.real_space_refine on Sun Feb 18 20:12:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14182 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h15_34425/02_2024/8h15_34425.pdb" } resolution = 3.14182 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 120 5.16 5 C 14563 2.51 5 N 3757 2.21 5 O 4373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1121": "OD1" <-> "OD2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 850": "OD1" <-> "OD2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1074": "OE1" <-> "OE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C ASP 613": "OD1" <-> "OD2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 762": "OE1" <-> "OE2" Residue "C TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 932": "OD1" <-> "OD2" Residue "C ASP 961": "OD1" <-> "OD2" Residue "C GLU 972": "OE1" <-> "OE2" Residue "C ASP 976": "OD1" <-> "OD2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1054": "OE1" <-> "OE2" Residue "C GLU 1066": "OE1" <-> "OE2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1121": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7565 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 43, 'TRANS': 924} Chain breaks: 12 Chain: "B" Number of atoms: 7480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7480 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 42, 'TRANS': 915} Chain breaks: 11 Chain: "C" Number of atoms: 7516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7516 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 43, 'TRANS': 918} Chain breaks: 12 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.31, per 1000 atoms: 0.50 Number of scatterers: 22813 At special positions: 0 Unit cell: (126.9, 132.3, 155.25, 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 120 16.00 O 4373 8.00 N 3757 7.00 C 14563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.06 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=1.99 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.06 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.05 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.05 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=1.98 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 227 " " NAG A1302 " - " ASN A 269 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1080 " " NAG B1301 " - " ASN B1080 " " NAG B1302 " - " ASN B 158 " " NAG B1303 " - " ASN B 227 " " NAG B1304 " - " ASN B 318 " " NAG B1305 " - " ASN B 699 " " NAG B1306 " - " ASN B 783 " " NAG C1301 " - " ASN C1080 " " NAG C1302 " - " ASN C 227 " " NAG C1303 " - " ASN C 318 " " NAG C1304 " - " ASN C 699 " " NAG C1305 " - " ASN C 783 " " NAG C1306 " - " ASN C1116 " " NAG C1307 " - " ASN C 269 " Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 4.4 seconds 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5420 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 25.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.539A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.763A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.182A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 394 through 398 removed outlier: 4.016A pdb=" N ALA A 398 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 736 through 739 removed outlier: 3.618A pdb=" N GLY A 739 " --> pdb=" O LEU A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 741 through 765 Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.637A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.517A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.293A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 removed outlier: 3.656A pdb=" N GLU B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 4.118A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.256A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.802A pdb=" N ASN B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.593A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.736A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.510A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.432A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.526A pdb=" N GLU C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.976A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 4.224A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.264A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 602 through 612 removed outlier: 4.069A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.768A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.743A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 867 Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.641A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.925A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.521A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.146A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.552A pdb=" N HIS A 33 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.785A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.380A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.193A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 165 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.995A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.552A pdb=" N PHE A 527 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.530A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.707A pdb=" N PHE A 379 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 685 removed outlier: 3.558A pdb=" N SER A 685 " --> pdb=" O MET B 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 695 removed outlier: 3.995A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.723A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.532A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 770 removed outlier: 3.564A pdb=" N MET A 770 " --> pdb=" O ALA C 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.591A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.940A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.835A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.105A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 128 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 122 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 297 through 306 removed outlier: 7.042A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.602A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 420 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 365 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.555A pdb=" N SER B 659 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 683 through 685 removed outlier: 7.116A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 695 removed outlier: 4.405A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.548A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.548A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.592A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.157A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 187 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 88 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.941A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.962A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 101 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 297 through 306 removed outlier: 6.962A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 634 " --> pdb=" O THR C 631 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AE3, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.691A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 422 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 640 through 641 removed outlier: 3.560A pdb=" N SER C 659 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.302A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.743A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.571A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 717 " --> pdb=" O THR C 841 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF2, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 5.334A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.47 Time building geometry restraints manager: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7289 1.34 - 1.48: 6561 1.48 - 1.62: 9286 1.62 - 1.76: 16 1.76 - 1.90: 146 Bond restraints: 23298 Sorted by residual: bond pdb=" C LYS B 411 " pdb=" N LEU B 412 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.07e-02 2.33e+03 1.08e+01 bond pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " ideal model delta sigma weight residual 1.808 1.703 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " ideal model delta sigma weight residual 1.808 1.708 0.100 3.30e-02 9.18e+02 9.12e+00 bond pdb=" CG LEU B 898 " pdb=" CD1 LEU B 898 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.01e+00 bond pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " ideal model delta sigma weight residual 1.808 1.898 -0.090 3.30e-02 9.18e+02 7.46e+00 ... (remaining 23293 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.96: 395 104.96 - 112.43: 11503 112.43 - 119.91: 8472 119.91 - 127.38: 11090 127.38 - 134.85: 179 Bond angle restraints: 31639 Sorted by residual: angle pdb=" CA CYS A 378 " pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " ideal model delta sigma weight residual 114.40 134.85 -20.45 2.30e+00 1.89e-01 7.90e+01 angle pdb=" CA CYS B 378 " pdb=" CB CYS B 378 " pdb=" SG CYS B 378 " ideal model delta sigma weight residual 114.40 130.32 -15.92 2.30e+00 1.89e-01 4.79e+01 angle pdb=" N GLY C1081 " pdb=" CA GLY C1081 " pdb=" C GLY C1081 " ideal model delta sigma weight residual 113.58 106.65 6.93 1.07e+00 8.73e-01 4.19e+01 angle pdb=" CA CYS A 511 " pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " ideal model delta sigma weight residual 114.40 129.07 -14.67 2.30e+00 1.89e-01 4.07e+01 angle pdb=" CA CYS B 419 " pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " ideal model delta sigma weight residual 114.40 128.94 -14.54 2.30e+00 1.89e-01 3.99e+01 ... (remaining 31634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12744 18.00 - 36.00: 1132 36.00 - 53.99: 192 53.99 - 71.99: 39 71.99 - 89.99: 20 Dihedral angle restraints: 14127 sinusoidal: 5726 harmonic: 8401 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 11.42 81.58 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -16.98 -69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA CYS B 603 " pdb=" C CYS B 603 " pdb=" N THR B 604 " pdb=" CA THR B 604 " ideal model delta harmonic sigma weight residual 180.00 143.74 36.26 0 5.00e+00 4.00e-02 5.26e+01 ... (remaining 14124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3596 0.160 - 0.321: 57 0.321 - 0.481: 5 0.481 - 0.641: 0 0.641 - 0.801: 1 Chirality restraints: 3659 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 227 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL C 606 " pdb=" CA VAL C 606 " pdb=" CG1 VAL C 606 " pdb=" CG2 VAL C 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CG LEU C 898 " pdb=" CB LEU C 898 " pdb=" CD1 LEU C 898 " pdb=" CD2 LEU C 898 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3656 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 227 " 0.003 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" CG ASN C 227 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 227 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 227 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 323 " 0.063 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO A 324 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 158 " 0.029 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN B 158 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 158 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 158 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.035 2.00e-02 2.50e+03 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1526 2.73 - 3.27: 19718 3.27 - 3.81: 33566 3.81 - 4.36: 41903 4.36 - 4.90: 76858 Nonbonded interactions: 173571 Sorted by model distance: nonbonded pdb=" O SER A 380 " pdb=" OG1 THR A 509 " model vdw 2.182 2.440 nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.191 2.440 nonbonded pdb=" O SER A 35 " pdb=" OG SER A 35 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR A1098 " pdb=" OD1 ASP A1100 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR A 698 " pdb=" O GLN A1053 " model vdw 2.254 2.440 ... (remaining 173566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 131 or resid 155 through 235 or resid 250 throu \ gh 425 or resid 439 through 455 or resid 492 through 810 or resid 818 through 82 \ 3 or resid 832 through 1121 or resid 1301 through 1305)) selection = (chain 'B' and (resid 31 through 131 or resid 155 through 166 or resid 181 throu \ gh 810 or resid 818 through 1121 or resid 1301 through 1305)) selection = (chain 'C' and (resid 31 through 235 or resid 250 through 425 or resid 439 throu \ gh 455 or resid 492 through 1121 or resid 1301 through 1305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 4.740 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 61.740 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.011 0.123 23298 Z= 0.730 Angle : 1.033 20.448 31639 Z= 0.553 Chirality : 0.068 0.801 3659 Planarity : 0.007 0.092 4048 Dihedral : 14.032 89.990 8590 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 2812 helix: -0.33 (0.19), residues: 658 sheet: -0.08 (0.20), residues: 661 loop : -2.19 (0.13), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 868 HIS 0.010 0.002 HIS C1046 PHE 0.038 0.004 PHE C 527 TYR 0.036 0.003 TYR B 200 ARG 0.016 0.001 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.482 Fit side-chains REVERT: A 183 ARG cc_start: 0.7370 (ptp-110) cc_final: 0.7168 (mtp180) REVERT: A 1032 MET cc_start: 0.8811 (ptm) cc_final: 0.8510 (ptm) REVERT: B 99 ARG cc_start: 0.6339 (ptt180) cc_final: 0.6139 (mtp85) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3447 time to fit residues: 136.5261 Evaluate side-chains 222 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 260 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 835 GLN C 523 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23298 Z= 0.191 Angle : 0.572 12.641 31639 Z= 0.303 Chirality : 0.046 0.356 3659 Planarity : 0.005 0.056 4048 Dihedral : 6.299 59.786 3458 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.48 % Allowed : 6.82 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2812 helix: 1.08 (0.20), residues: 669 sheet: 0.40 (0.20), residues: 673 loop : -1.92 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.003 0.001 HIS C1046 PHE 0.016 0.001 PHE B 387 TYR 0.016 0.001 TYR A 200 ARG 0.005 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 2.655 Fit side-chains REVERT: A 352 TYR cc_start: 0.8155 (m-80) cc_final: 0.7256 (m-80) REVERT: A 1032 MET cc_start: 0.8838 (ptm) cc_final: 0.8537 (ptm) REVERT: A 1074 GLU cc_start: 0.7026 (pt0) cc_final: 0.6688 (pt0) REVERT: A 1101 ASN cc_start: 0.7838 (p0) cc_final: 0.7432 (p0) REVERT: B 99 ARG cc_start: 0.6290 (ptt180) cc_final: 0.5803 (ptp-110) REVERT: B 882 MET cc_start: 0.8501 (mtt) cc_final: 0.8254 (mtm) REVERT: C 160 THR cc_start: 0.7705 (p) cc_final: 0.7065 (t) REVERT: C 183 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.6926 (mtt180) REVERT: C 550 GLN cc_start: 0.7304 (tp40) cc_final: 0.7028 (tp40) outliers start: 12 outliers final: 8 residues processed: 244 average time/residue: 0.3454 time to fit residues: 133.8984 Evaluate side-chains 219 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 216 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 261 optimal weight: 0.1980 chunk 282 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 258 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN B 108 ASN C 523 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23298 Z= 0.172 Angle : 0.519 10.965 31639 Z= 0.274 Chirality : 0.045 0.296 3659 Planarity : 0.004 0.046 4048 Dihedral : 5.728 59.556 3458 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.44 % Allowed : 8.42 % Favored : 90.14 % 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: -0.44 (0.15), residues: 2812 helix: 1.80 (0.21), residues: 655 sheet: 0.53 (0.20), residues: 680 loop : -1.78 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 PHE 0.015 0.001 PHE A 83 TYR 0.016 0.001 TYR C1049 ARG 0.005 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 234 time to evaluate : 2.616 Fit side-chains REVERT: A 352 TYR cc_start: 0.8128 (m-80) cc_final: 0.7272 (m-80) REVERT: A 1032 MET cc_start: 0.8824 (ptm) cc_final: 0.8526 (ptm) REVERT: A 1074 GLU cc_start: 0.7126 (pt0) cc_final: 0.6801 (pt0) REVERT: B 99 ARG cc_start: 0.6276 (ptt180) cc_final: 0.5781 (ptp-110) REVERT: B 796 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7574 (mmtm) REVERT: B 882 MET cc_start: 0.8519 (mtt) cc_final: 0.8288 (mtm) REVERT: C 110 LYS cc_start: 0.8159 (ptpp) cc_final: 0.7854 (tptt) REVERT: C 160 THR cc_start: 0.7043 (p) cc_final: 0.6644 (t) REVERT: C 183 ARG cc_start: 0.7258 (ptp-170) cc_final: 0.7007 (mtt180) outliers start: 36 outliers final: 24 residues processed: 259 average time/residue: 0.3371 time to fit residues: 140.2292 Evaluate side-chains 239 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 248 optimal weight: 0.0980 chunk 74 optimal weight: 0.0770 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 523 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 23298 Z= 0.246 Angle : 0.562 13.289 31639 Z= 0.294 Chirality : 0.046 0.278 3659 Planarity : 0.004 0.044 4048 Dihedral : 5.805 59.685 3458 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.64 % Allowed : 9.86 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2812 helix: 1.80 (0.21), residues: 650 sheet: 0.64 (0.20), residues: 673 loop : -1.81 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 868 HIS 0.004 0.001 HIS C1046 PHE 0.019 0.002 PHE A 83 TYR 0.018 0.001 TYR C1049 ARG 0.005 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 2.637 Fit side-chains REVERT: A 352 TYR cc_start: 0.8150 (m-80) cc_final: 0.7342 (m-80) REVERT: A 1032 MET cc_start: 0.8898 (ptm) cc_final: 0.8592 (ptm) REVERT: A 1074 GLU cc_start: 0.7075 (pt0) cc_final: 0.6747 (pt0) REVERT: B 99 ARG cc_start: 0.6302 (ptt180) cc_final: 0.5811 (ptp-110) REVERT: B 796 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7587 (mmtm) REVERT: B 959 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 110 LYS cc_start: 0.8113 (ptpp) cc_final: 0.7781 (tptt) REVERT: C 160 THR cc_start: 0.7158 (p) cc_final: 0.6727 (t) REVERT: C 183 ARG cc_start: 0.7231 (ptp-170) cc_final: 0.6993 (mtt180) outliers start: 41 outliers final: 35 residues processed: 251 average time/residue: 0.3194 time to fit residues: 129.1729 Evaluate side-chains 248 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 5.9990 chunk 157 optimal weight: 0.0040 chunk 4 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 236 optimal weight: 0.0270 chunk 191 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 523 GLN B 108 ASN B 746 ASN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23298 Z= 0.166 Angle : 0.502 10.604 31639 Z= 0.264 Chirality : 0.044 0.269 3659 Planarity : 0.004 0.041 4048 Dihedral : 5.531 59.983 3458 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.88 % Allowed : 10.89 % Favored : 87.23 % 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: -0.27 (0.16), residues: 2812 helix: 2.20 (0.21), residues: 645 sheet: 0.59 (0.20), residues: 679 loop : -1.74 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.002 0.000 HIS A1030 PHE 0.013 0.001 PHE A 83 TYR 0.016 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 2.653 Fit side-chains REVERT: A 183 ARG cc_start: 0.7400 (ptp-170) cc_final: 0.7169 (mtt180) REVERT: A 352 TYR cc_start: 0.8128 (m-80) cc_final: 0.7372 (m-80) REVERT: A 1032 MET cc_start: 0.8814 (ptm) cc_final: 0.8532 (ptm) REVERT: A 1074 GLU cc_start: 0.7053 (pt0) cc_final: 0.6752 (pt0) REVERT: B 99 ARG cc_start: 0.6295 (ptt180) cc_final: 0.5798 (ptp-110) REVERT: B 796 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7602 (mmtm) REVERT: C 110 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7648 (tptt) REVERT: C 183 ARG cc_start: 0.7262 (ptp-170) cc_final: 0.7003 (mtt180) outliers start: 47 outliers final: 35 residues processed: 263 average time/residue: 0.3282 time to fit residues: 139.8241 Evaluate side-chains 250 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 523 GLN B 108 ASN C 786 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23298 Z= 0.262 Angle : 0.571 14.968 31639 Z= 0.298 Chirality : 0.046 0.262 3659 Planarity : 0.004 0.044 4048 Dihedral : 5.730 59.705 3458 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.08 % Allowed : 11.41 % Favored : 86.51 % 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: -0.36 (0.16), residues: 2812 helix: 1.89 (0.21), residues: 649 sheet: 0.67 (0.20), residues: 677 loop : -1.77 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 868 HIS 0.005 0.001 HIS C1046 PHE 0.021 0.002 PHE A 83 TYR 0.018 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 2.480 Fit side-chains REVERT: A 352 TYR cc_start: 0.8147 (m-80) cc_final: 0.7334 (m-80) REVERT: A 1032 MET cc_start: 0.8891 (ptm) cc_final: 0.8580 (ptm) REVERT: A 1074 GLU cc_start: 0.7091 (pt0) cc_final: 0.6774 (pt0) REVERT: B 99 ARG cc_start: 0.6332 (ptt180) cc_final: 0.5826 (ptp-110) REVERT: B 796 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7606 (mmtm) REVERT: B 959 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 110 LYS cc_start: 0.8041 (ptpp) cc_final: 0.7694 (tptt) REVERT: C 183 ARG cc_start: 0.7315 (ptp-170) cc_final: 0.7023 (mtt180) outliers start: 52 outliers final: 43 residues processed: 256 average time/residue: 0.3032 time to fit residues: 126.3288 Evaluate side-chains 259 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 233 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 937 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 23298 Z= 0.325 Angle : 0.617 14.604 31639 Z= 0.321 Chirality : 0.048 0.253 3659 Planarity : 0.004 0.043 4048 Dihedral : 5.952 59.695 3458 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.15 % Allowed : 11.77 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2812 helix: 1.64 (0.20), residues: 647 sheet: 0.75 (0.21), residues: 654 loop : -1.83 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 868 HIS 0.005 0.001 HIS C1046 PHE 0.023 0.002 PHE A 83 TYR 0.018 0.002 TYR C1049 ARG 0.006 0.001 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 224 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 352 TYR cc_start: 0.8215 (m-80) cc_final: 0.7419 (m-80) REVERT: A 1032 MET cc_start: 0.8878 (ptm) cc_final: 0.8567 (ptm) REVERT: A 1074 GLU cc_start: 0.7056 (pt0) cc_final: 0.6721 (pt0) REVERT: B 99 ARG cc_start: 0.6380 (ptt180) cc_final: 0.5876 (ptp-110) REVERT: B 796 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7606 (mmtm) REVERT: B 959 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 110 LYS cc_start: 0.8034 (ptpp) cc_final: 0.7710 (tptt) REVERT: C 183 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7064 (mtt180) outliers start: 54 outliers final: 45 residues processed: 265 average time/residue: 0.3244 time to fit residues: 138.5060 Evaluate side-chains 264 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 937 ASN C 744 GLN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23298 Z= 0.203 Angle : 0.536 13.924 31639 Z= 0.281 Chirality : 0.045 0.257 3659 Planarity : 0.004 0.042 4048 Dihedral : 5.694 59.655 3458 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.15 % Allowed : 12.17 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2812 helix: 1.96 (0.21), residues: 650 sheet: 0.80 (0.21), residues: 653 loop : -1.76 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 868 HIS 0.002 0.001 HIS A1046 PHE 0.016 0.001 PHE A 83 TYR 0.016 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 223 time to evaluate : 2.507 Fit side-chains revert: symmetry clash REVERT: A 352 TYR cc_start: 0.8163 (m-80) cc_final: 0.7355 (m-80) REVERT: A 898 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 1032 MET cc_start: 0.8844 (ptm) cc_final: 0.8531 (ptm) REVERT: A 1074 GLU cc_start: 0.7043 (pt0) cc_final: 0.6702 (pt0) REVERT: B 99 ARG cc_start: 0.6375 (ptt180) cc_final: 0.5868 (ptp-110) REVERT: B 796 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7607 (mmtm) REVERT: B 959 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8298 (mp) REVERT: C 110 LYS cc_start: 0.8022 (ptpp) cc_final: 0.7668 (tptt) REVERT: C 183 ARG cc_start: 0.7328 (ptp-170) cc_final: 0.7049 (mtt180) REVERT: C 1068 LYS cc_start: 0.8128 (pttm) cc_final: 0.7873 (mtmt) outliers start: 54 outliers final: 48 residues processed: 263 average time/residue: 0.3261 time to fit residues: 138.1545 Evaluate side-chains 266 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 241 optimal weight: 0.0170 chunk 257 optimal weight: 0.5980 chunk 264 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 523 GLN B 108 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 23298 Z= 0.157 Angle : 0.500 13.604 31639 Z= 0.262 Chirality : 0.044 0.268 3659 Planarity : 0.004 0.041 4048 Dihedral : 5.369 59.869 3458 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.19 % Allowed : 12.25 % Favored : 85.55 % 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: -0.12 (0.16), residues: 2812 helix: 2.25 (0.21), residues: 651 sheet: 0.76 (0.21), residues: 669 loop : -1.66 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 PHE 0.013 0.001 PHE C1103 TYR 0.016 0.001 TYR C1049 ARG 0.007 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7147 (mtt180) REVERT: A 352 TYR cc_start: 0.8129 (m-80) cc_final: 0.7368 (m-80) REVERT: A 889 ASN cc_start: 0.7766 (t0) cc_final: 0.7189 (t0) REVERT: A 1032 MET cc_start: 0.8839 (ptm) cc_final: 0.8561 (ptm) REVERT: A 1059 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8819 (t) REVERT: B 99 ARG cc_start: 0.6366 (ptt180) cc_final: 0.6101 (mtp85) REVERT: B 796 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7604 (mmtm) REVERT: C 110 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7754 (tptt) REVERT: C 183 ARG cc_start: 0.7268 (ptp-170) cc_final: 0.7012 (mtt180) outliers start: 55 outliers final: 49 residues processed: 266 average time/residue: 0.3101 time to fit residues: 133.5193 Evaluate side-chains 269 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 523 GLN B 108 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23298 Z= 0.237 Angle : 0.548 13.354 31639 Z= 0.286 Chirality : 0.046 0.263 3659 Planarity : 0.004 0.043 4048 Dihedral : 5.520 59.681 3458 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.23 % Allowed : 12.37 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.20 (0.16), residues: 2812 helix: 2.08 (0.21), residues: 650 sheet: 0.83 (0.21), residues: 660 loop : -1.70 (0.14), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 868 HIS 0.004 0.001 HIS C1046 PHE 0.019 0.002 PHE A 83 TYR 0.018 0.001 TYR C1049 ARG 0.007 0.000 ARG B 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 225 time to evaluate : 2.600 Fit side-chains revert: symmetry clash REVERT: A 352 TYR cc_start: 0.8174 (m-80) cc_final: 0.7399 (m-80) REVERT: A 1032 MET cc_start: 0.8884 (ptm) cc_final: 0.8568 (ptm) REVERT: A 1059 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8771 (t) REVERT: B 796 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7600 (mmtm) REVERT: C 110 LYS cc_start: 0.8085 (ptpp) cc_final: 0.7785 (tptt) REVERT: C 183 ARG cc_start: 0.7286 (ptp-170) cc_final: 0.7019 (mtt180) REVERT: C 1068 LYS cc_start: 0.8156 (pttm) cc_final: 0.7912 (mtmt) outliers start: 56 outliers final: 52 residues processed: 267 average time/residue: 0.3253 time to fit residues: 139.5828 Evaluate side-chains 272 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 chunk 209 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 523 GLN B 108 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.125488 restraints weight = 24714.944| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.52 r_work: 0.3022 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 23298 Z= 0.145 Angle : 0.491 12.952 31639 Z= 0.258 Chirality : 0.044 0.269 3659 Planarity : 0.004 0.041 4048 Dihedral : 5.202 59.348 3458 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.19 % Allowed : 12.53 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2812 helix: 2.49 (0.21), residues: 642 sheet: 0.83 (0.21), residues: 656 loop : -1.58 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 PHE 0.025 0.001 PHE B 220 TYR 0.015 0.001 TYR C1049 ARG 0.007 0.000 ARG B 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.14 seconds wall clock time: 79 minutes 48.52 seconds (4788.52 seconds total)