Starting phenix.real_space_refine on Wed Mar 20 10:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh9_40038/03_2024/8gh9_40038.pdb" } resolution = 3.8 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= 0.009 sd= 0.063 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 178 5.16 5 C 17569 2.51 5 N 4401 2.21 5 O 4918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C ASP 726": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1047": "OD1" <-> "OD2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ASP 726": "OD1" <-> "OD2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "D GLU 1040": "OE1" <-> "OE2" Residue "D ASP 1047": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27066 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6644 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 830, 6636 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 804} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 830, 6636 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 804} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6779 Chain: "C" Number of atoms: 6900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 866, 6892 Classifications: {'peptide': 866} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 838} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 866, 6892 Classifications: {'peptide': 866} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 838} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7041 Chain: "B" Number of atoms: 6651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 831, 6643 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 805} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 831, 6643 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 805} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6786 Chain: "D" Number of atoms: 6871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 862, 6863 Classifications: {'peptide': 862} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 834} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 862, 6863 Classifications: {'peptide': 862} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 834} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7010 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.45 residue: pdb=" N AASN C 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.41 residue: pdb=" N AASN B 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.45 residue: pdb=" N AASN D 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.41 Time building chain proxies: 24.45, per 1000 atoms: 0.90 Number of scatterers: 27066 At special positions: 0 Unit cell: (152.28, 150.12, 132.84, 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 178 16.00 O 4918 8.00 N 4401 7.00 C 17569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 10.04 Conformation dependent library (CDL) restraints added in 9.0 seconds 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6450 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 20 sheets defined 50.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.386A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.542A pdb=" N ASN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 170 removed outlier: 4.206A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.222A pdb=" N LEU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 260 removed outlier: 3.763A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 4.200A pdb=" N CYS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 4.331A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.704A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.933A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.677A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 500 removed outlier: 3.578A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.641A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.816A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.751A pdb=" N LEU A 751 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.598A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.503A pdb=" N LEU A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 892' Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.600A pdb=" N LEU A 905 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.657A pdb=" N THR A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 922 through 930 removed outlier: 4.158A pdb=" N PHE A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 941 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'C' and resid 21 through 26 removed outlier: 4.488A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.683A pdb=" N PHE C 34 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.845A pdb=" N GLY C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 170 removed outlier: 4.225A pdb=" N TYR C 163 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 232 through 260 removed outlier: 4.011A pdb=" N GLY C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.221A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.163A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.657A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.542A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.328A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.616A pdb=" N LEU C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 removed outlier: 4.024A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O TYR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.396A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.648A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 797 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 4.145A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 removed outlier: 3.669A pdb=" N LEU C 905 " --> pdb=" O GLU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 902 through 905' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.311A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 969 through 973 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.318A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'B' and resid 22 through 29 removed outlier: 3.536A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 109 through 134 removed outlier: 4.575A pdb=" N LEU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 170 removed outlier: 3.658A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 180 through 199 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 207 through 211 removed outlier: 4.163A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 260 removed outlier: 3.623A pdb=" N ILE B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 319 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 432 through 451 removed outlier: 4.042A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 486 through 500 removed outlier: 4.374A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.552A pdb=" N LEU B 510 " --> pdb=" O MET B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.997A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 4.508A pdb=" N VAL B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.605A pdb=" N ARG B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.841A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 791 Processing helix chain 'B' and resid 804 through 808 removed outlier: 3.614A pdb=" N GLN B 807 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN B 808 " --> pdb=" O ALA B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 808' Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.826A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.773A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 890 " --> pdb=" O ASN B 887 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 916 through 921 removed outlier: 3.620A pdb=" N VAL B 919 " --> pdb=" O ALA B 916 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 removed outlier: 4.173A pdb=" N PHE B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 3.886A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 957 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.556A pdb=" N ALA D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.992A pdb=" N THR D 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 122 through 136 removed outlier: 3.601A pdb=" N LEU D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 170 removed outlier: 4.017A pdb=" N ASN D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 163 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.827A pdb=" N GLU D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 260 removed outlier: 3.970A pdb=" N SER D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 297 through 318 removed outlier: 4.591A pdb=" N ALA D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.044A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.705A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.816A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.257A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 601 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.981A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 removed outlier: 3.583A pdb=" N LEU D 751 " --> pdb=" O TYR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.701A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 891 removed outlier: 4.066A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 removed outlier: 3.613A pdb=" N LEU D 905 " --> pdb=" O GLU D 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 902 through 905' Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.348A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.541A pdb=" N ARG D 972 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 4.307A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 378 removed outlier: 7.442A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 457 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 539 removed outlier: 3.871A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 778 removed outlier: 6.340A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id=AA5, first strand: chain 'C' and resid 398 through 399 removed outlier: 7.252A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 538 removed outlier: 3.557A pdb=" N ILE C 598 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 567 through 569 Processing sheet with id=AA8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.344A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 757 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 799 " --> pdb=" O HIS C 718 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 879 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 976 through 979 removed outlier: 4.304A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.719A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 377 removed outlier: 7.723A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 457 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN B 459 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 539 removed outlier: 7.174A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.963A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 975 through 976 Processing sheet with id=AB6, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 376 removed outlier: 6.175A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.809A pdb=" N GLY D 595 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.214A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 757 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS D 718 " --> pdb=" O MET D 799 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL D 801 " --> pdb=" O HIS D 718 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 981 removed outlier: 4.056A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2956 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: 8.54 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8534 1.34 - 1.46: 6783 1.46 - 1.58: 12103 1.58 - 1.70: 0 1.70 - 1.82: 268 Bond restraints: 27688 Sorted by residual: bond pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.37e+00 bond pdb=" CB ASN B 806 " pdb=" CG ASN B 806 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.35e+00 bond pdb=" CB ASP D 726 " pdb=" CG ASP D 726 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" CB GLN B 807 " pdb=" CG GLN B 807 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB ASN B 795 " pdb=" CG ASN B 795 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 27683 not shown) Histogram of bond angle deviations from ideal: 96.63 - 104.14: 317 104.14 - 111.64: 12570 111.64 - 119.15: 9937 119.15 - 126.65: 14337 126.65 - 134.15: 406 Bond angle restraints: 37567 Sorted by residual: angle pdb=" C SER D 286 " pdb=" CA SER D 286 " pdb=" CB SER D 286 " ideal model delta sigma weight residual 116.63 110.65 5.98 1.16e+00 7.43e-01 2.65e+01 angle pdb=" CB MET D1009 " pdb=" CG MET D1009 " pdb=" SD MET D1009 " ideal model delta sigma weight residual 112.70 127.24 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CA LEU C 161 " pdb=" CB LEU C 161 " pdb=" CG LEU C 161 " ideal model delta sigma weight residual 116.30 131.83 -15.53 3.50e+00 8.16e-02 1.97e+01 angle pdb=" CA LEU C 206 " pdb=" CB LEU C 206 " pdb=" CG LEU C 206 " ideal model delta sigma weight residual 116.30 131.70 -15.40 3.50e+00 8.16e-02 1.94e+01 angle pdb=" CB MET D 282 " pdb=" CG MET D 282 " pdb=" SD MET D 282 " ideal model delta sigma weight residual 112.70 124.92 -12.22 3.00e+00 1.11e-01 1.66e+01 ... (remaining 37562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13834 17.94 - 35.88: 1892 35.88 - 53.81: 512 53.81 - 71.75: 61 71.75 - 89.69: 22 Dihedral angle restraints: 16321 sinusoidal: 6373 harmonic: 9948 Sorted by residual: dihedral pdb=" CA ASN C1008 " pdb=" C ASN C1008 " pdb=" N MET C1009 " pdb=" CA MET C1009 " ideal model delta harmonic sigma weight residual 180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU A 321 " pdb=" C GLU A 321 " pdb=" N ILE A 322 " pdb=" CA ILE A 322 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA THR D 352 " pdb=" C THR D 352 " pdb=" N LEU D 353 " pdb=" CA LEU D 353 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 16318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3262 0.049 - 0.099: 824 0.099 - 0.148: 207 0.148 - 0.198: 8 0.198 - 0.247: 1 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CB ILE D 456 " pdb=" CA ILE D 456 " pdb=" CG1 ILE D 456 " pdb=" CG2 ILE D 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA LEU C 161 " pdb=" N LEU C 161 " pdb=" C LEU C 161 " pdb=" CB LEU C 161 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 806 " pdb=" N ASN B 806 " pdb=" C ASN B 806 " pdb=" CB ASN B 806 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 4299 not shown) Planarity restraints: 4717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1055 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C PHE A1055 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE A1055 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A1056 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " -0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO A 192 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 191 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO C 192 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " 0.034 5.00e-02 4.00e+02 ... (remaining 4714 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1208 2.72 - 3.26: 28002 3.26 - 3.81: 43720 3.81 - 4.35: 49895 4.35 - 4.90: 83824 Nonbonded interactions: 206649 Sorted by model distance: nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR B 290 " model vdw 2.171 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR B 273 " pdb=" OE1 GLU B 276 " model vdw 2.207 2.440 nonbonded pdb=" O THR B 935 " pdb=" OG1 THR B 939 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU C 417 " pdb=" OH TYR C 450 " model vdw 2.248 2.440 ... (remaining 206644 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 19 through 33 or resid 97 through 368 or resid 371 through \ 825 or resid 827 through 1056)) selection = (chain 'B' and (resid 19 through 33 or resid 97 through 368 or resid 371 through \ 825 or resid 827 through 976 or resid 995 through 1056)) selection = (chain 'C' and (resid 19 through 33 or resid 97 through 368 or resid 371 through \ 570 or resid 591 through 825 or resid 827 through 958 or resid 964 through 976 \ or resid 995 through 1056)) selection = (chain 'D' and (resid 19 through 33 or resid 97 through 570 or resid 591 through \ 825 or resid 827 through 958 or resid 964 through 976 or resid 995 through 1056 \ )) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.960 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: 5.230 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 83.530 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 95.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.004 0.049 27688 Z= 0.247 Angle : 0.751 15.526 37567 Z= 0.371 Chirality : 0.045 0.247 4302 Planarity : 0.005 0.064 4717 Dihedral : 17.392 89.691 9871 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.37 % Allowed : 35.22 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3351 helix: -0.29 (0.13), residues: 1500 sheet: -1.36 (0.30), residues: 347 loop : -1.64 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 246 HIS 0.011 0.001 HIS A 350 PHE 0.035 0.002 PHE A 252 TYR 0.036 0.001 TYR D 145 ARG 0.017 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 346 time to evaluate : 3.222 Fit side-chains revert: symmetry clash REVERT: C 159 PHE cc_start: 0.8947 (t80) cc_final: 0.8300 (t80) REVERT: B 303 PHE cc_start: 0.8890 (m-80) cc_final: 0.8668 (m-10) REVERT: D 145 TYR cc_start: 0.6989 (m-80) cc_final: 0.6773 (m-80) outliers start: 11 outliers final: 7 residues processed: 355 average time/residue: 0.3302 time to fit residues: 196.1248 Evaluate side-chains 344 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 337 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 1000 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 142 optimal weight: 0.0040 chunk 87 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 200 ASN A 222 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 534 ASN A 749 HIS A 793 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN C 142 GLN C 143 ASN C 397 GLN C 449 ASN C 462 GLN C 979 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 465 ASN B 468 HIS B 496 GLN B 509 ASN B 534 ASN B 745 ASN B 793 ASN ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 225 ASN D 365 HIS D 397 GLN D 402 GLN D 449 ASN D 534 ASN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN D1021 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27688 Z= 0.341 Angle : 0.659 10.831 37567 Z= 0.334 Chirality : 0.044 0.172 4302 Planarity : 0.004 0.060 4717 Dihedral : 4.886 54.025 3630 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.52 % Allowed : 32.11 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3351 helix: -0.10 (0.14), residues: 1491 sheet: -1.66 (0.29), residues: 359 loop : -1.59 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 246 HIS 0.005 0.001 HIS D 749 PHE 0.018 0.002 PHE A 159 TYR 0.035 0.002 TYR B 279 ARG 0.010 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 330 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: C 159 PHE cc_start: 0.8915 (t80) cc_final: 0.8274 (t80) REVERT: C 982 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 145 TYR cc_start: 0.7082 (m-80) cc_final: 0.6783 (m-10) REVERT: D 303 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8475 (t80) REVERT: D 307 PHE cc_start: 0.8587 (m-80) cc_final: 0.7393 (m-80) outliers start: 135 outliers final: 86 residues processed: 425 average time/residue: 0.3330 time to fit residues: 239.3654 Evaluate side-chains 411 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 322 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1052 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 40.0000 chunk 95 optimal weight: 30.0000 chunk 255 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 307 optimal weight: 0.0870 chunk 332 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 overall best weight: 4.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN D 402 GLN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27688 Z= 0.341 Angle : 0.664 11.968 37567 Z= 0.334 Chirality : 0.044 0.169 4302 Planarity : 0.004 0.059 4717 Dihedral : 4.860 44.711 3625 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.28 % Allowed : 31.81 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3351 helix: -0.09 (0.14), residues: 1500 sheet: -1.83 (0.29), residues: 351 loop : -1.62 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 176 HIS 0.005 0.001 HIS D 749 PHE 0.028 0.002 PHE C 160 TYR 0.017 0.001 TYR D 332 ARG 0.009 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 325 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8160 (m-80) cc_final: 0.7655 (m-80) REVERT: A 378 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7989 (tt) REVERT: A 564 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8323 (tt) REVERT: C 159 PHE cc_start: 0.8915 (t80) cc_final: 0.8080 (m-80) REVERT: C 160 PHE cc_start: 0.8296 (m-80) cc_final: 0.8014 (m-80) REVERT: C 307 PHE cc_start: 0.8574 (m-80) cc_final: 0.8270 (m-80) REVERT: C 1009 MET cc_start: 0.8323 (mmm) cc_final: 0.7411 (mmm) REVERT: D 145 TYR cc_start: 0.7015 (m-80) cc_final: 0.6500 (m-80) REVERT: D 282 MET cc_start: 0.9011 (tpp) cc_final: 0.8694 (tpp) REVERT: D 303 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8407 (t80) REVERT: D 307 PHE cc_start: 0.8646 (m-80) cc_final: 0.7410 (m-80) REVERT: D 1004 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8379 (mm) outliers start: 158 outliers final: 107 residues processed: 440 average time/residue: 0.3243 time to fit residues: 239.7384 Evaluate side-chains 431 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 320 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 326 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27688 Z= 0.186 Angle : 0.596 14.736 37567 Z= 0.294 Chirality : 0.041 0.180 4302 Planarity : 0.004 0.058 4717 Dihedral : 4.599 47.362 3625 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.25 % Allowed : 32.81 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3351 helix: 0.14 (0.14), residues: 1493 sheet: -1.63 (0.29), residues: 359 loop : -1.54 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 PHE 0.026 0.001 PHE C 160 TYR 0.013 0.001 TYR A 401 ARG 0.007 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 345 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8134 (m-80) cc_final: 0.7491 (m-80) REVERT: A 321 GLU cc_start: 0.8722 (pm20) cc_final: 0.8442 (pm20) REVERT: A 564 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8356 (tt) REVERT: A 795 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8601 (t0) REVERT: C 159 PHE cc_start: 0.8898 (t80) cc_final: 0.8027 (m-80) REVERT: C 160 PHE cc_start: 0.8424 (m-80) cc_final: 0.8022 (m-80) REVERT: C 307 PHE cc_start: 0.8632 (m-80) cc_final: 0.8380 (m-80) REVERT: C 982 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7715 (pp) REVERT: C 1009 MET cc_start: 0.8310 (mmm) cc_final: 0.7420 (mmm) REVERT: B 156 PHE cc_start: 0.8251 (m-10) cc_final: 0.7530 (m-80) REVERT: B 393 ARG cc_start: 0.8379 (ptp90) cc_final: 0.7938 (ptp90) REVERT: B 806 ASN cc_start: 0.8560 (p0) cc_final: 0.8356 (p0) REVERT: D 145 TYR cc_start: 0.7127 (m-80) cc_final: 0.6470 (m-80) REVERT: D 282 MET cc_start: 0.8884 (tpp) cc_final: 0.8607 (tpp) REVERT: D 303 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8353 (t80) REVERT: D 307 PHE cc_start: 0.8705 (m-80) cc_final: 0.7333 (m-80) REVERT: D 402 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: D 513 MET cc_start: 0.7265 (tpt) cc_final: 0.6940 (tpp) REVERT: D 1004 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8369 (mm) outliers start: 127 outliers final: 84 residues processed: 442 average time/residue: 0.3324 time to fit residues: 246.0040 Evaluate side-chains 420 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 330 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 0.0770 chunk 185 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 278 optimal weight: 0.2980 chunk 225 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 166 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27688 Z= 0.210 Angle : 0.603 12.534 37567 Z= 0.298 Chirality : 0.042 0.165 4302 Planarity : 0.004 0.057 4717 Dihedral : 4.549 48.082 3623 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.55 % Allowed : 33.01 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3351 helix: 0.20 (0.14), residues: 1488 sheet: -1.61 (0.29), residues: 349 loop : -1.56 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 PHE 0.021 0.001 PHE A 217 TYR 0.026 0.001 TYR D1007 ARG 0.021 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 339 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8144 (m-80) cc_final: 0.7427 (m-80) REVERT: A 321 GLU cc_start: 0.8700 (pm20) cc_final: 0.8399 (pm20) REVERT: A 354 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: A 378 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 564 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8382 (tt) REVERT: A 795 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8595 (t0) REVERT: C 159 PHE cc_start: 0.8895 (t80) cc_final: 0.8027 (m-80) REVERT: C 160 PHE cc_start: 0.8437 (m-80) cc_final: 0.8057 (m-80) REVERT: C 303 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8412 (t80) REVERT: C 982 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7625 (pp) REVERT: C 1009 MET cc_start: 0.8277 (mmm) cc_final: 0.7813 (mmm) REVERT: B 156 PHE cc_start: 0.8296 (m-10) cc_final: 0.7578 (m-80) REVERT: D 145 TYR cc_start: 0.7202 (m-80) cc_final: 0.6472 (m-80) REVERT: D 303 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8344 (t80) REVERT: D 307 PHE cc_start: 0.8684 (m-80) cc_final: 0.7283 (m-80) REVERT: D 1004 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (mm) outliers start: 136 outliers final: 109 residues processed: 438 average time/residue: 0.3262 time to fit residues: 241.4415 Evaluate side-chains 449 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 332 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 327 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27688 Z= 0.177 Angle : 0.594 13.738 37567 Z= 0.292 Chirality : 0.041 0.174 4302 Planarity : 0.004 0.056 4717 Dihedral : 4.454 49.204 3622 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.68 % Allowed : 32.98 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3351 helix: 0.25 (0.14), residues: 1488 sheet: -1.50 (0.30), residues: 349 loop : -1.52 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 PHE 0.022 0.001 PHE A 217 TYR 0.021 0.001 TYR D 279 ARG 0.012 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 344 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8171 (m-80) cc_final: 0.7445 (m-80) REVERT: A 321 GLU cc_start: 0.8650 (pm20) cc_final: 0.8327 (pm20) REVERT: A 354 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 564 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 795 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 796 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8719 (mt) REVERT: C 159 PHE cc_start: 0.8870 (t80) cc_final: 0.7971 (m-80) REVERT: C 160 PHE cc_start: 0.8409 (m-80) cc_final: 0.8027 (m-80) REVERT: C 303 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8418 (t80) REVERT: C 423 LEU cc_start: 0.9020 (mp) cc_final: 0.8790 (mp) REVERT: C 982 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (pp) REVERT: C 1009 MET cc_start: 0.8223 (mmm) cc_final: 0.7948 (mmm) REVERT: B 353 LEU cc_start: 0.8341 (mt) cc_final: 0.7980 (tt) REVERT: B 393 ARG cc_start: 0.8344 (ptp90) cc_final: 0.7988 (ptp-170) REVERT: D 145 TYR cc_start: 0.7206 (m-80) cc_final: 0.6480 (m-80) REVERT: D 303 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8505 (t80) REVERT: D 1004 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8339 (mm) outliers start: 140 outliers final: 103 residues processed: 449 average time/residue: 0.3273 time to fit residues: 248.0647 Evaluate side-chains 442 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 331 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27688 Z= 0.154 Angle : 0.593 13.195 37567 Z= 0.288 Chirality : 0.041 0.174 4302 Planarity : 0.004 0.056 4717 Dihedral : 4.359 51.146 3622 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.18 % Allowed : 33.81 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3351 helix: 0.31 (0.14), residues: 1490 sheet: -1.36 (0.29), residues: 359 loop : -1.50 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 176 HIS 0.007 0.001 HIS A 350 PHE 0.024 0.001 PHE A 217 TYR 0.020 0.001 TYR D 279 ARG 0.005 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 349 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8154 (m-80) cc_final: 0.7391 (m-80) REVERT: A 564 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 159 PHE cc_start: 0.8875 (t80) cc_final: 0.7977 (m-80) REVERT: C 303 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8389 (t80) REVERT: C 423 LEU cc_start: 0.8942 (mp) cc_final: 0.8732 (mp) REVERT: C 799 MET cc_start: 0.7677 (tpp) cc_final: 0.7128 (tpt) REVERT: C 982 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7294 (pp) REVERT: C 1009 MET cc_start: 0.8199 (mmm) cc_final: 0.7893 (mmm) REVERT: B 353 LEU cc_start: 0.8360 (mt) cc_final: 0.8002 (tt) REVERT: B 806 ASN cc_start: 0.8737 (p0) cc_final: 0.8434 (p0) REVERT: D 145 TYR cc_start: 0.7236 (m-80) cc_final: 0.6530 (m-80) REVERT: D 303 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8497 (t80) REVERT: D 1004 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8338 (mm) outliers start: 125 outliers final: 99 residues processed: 438 average time/residue: 0.3197 time to fit residues: 235.6105 Evaluate side-chains 446 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 342 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 534 ASN C1036 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27688 Z= 0.145 Angle : 0.584 12.739 37567 Z= 0.285 Chirality : 0.041 0.172 4302 Planarity : 0.004 0.056 4717 Dihedral : 4.285 52.803 3622 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.95 % Allowed : 34.11 % Favored : 61.94 % 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: -0.96 (0.15), residues: 3351 helix: 0.37 (0.14), residues: 1491 sheet: -1.24 (0.30), residues: 359 loop : -1.47 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 176 HIS 0.007 0.001 HIS A 350 PHE 0.025 0.001 PHE A 217 TYR 0.024 0.001 TYR D1007 ARG 0.002 0.000 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 357 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8186 (m-80) cc_final: 0.7440 (m-80) REVERT: A 321 GLU cc_start: 0.8706 (pm20) cc_final: 0.8455 (pm20) REVERT: A 564 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8400 (tt) REVERT: C 159 PHE cc_start: 0.8910 (t80) cc_final: 0.8024 (m-80) REVERT: C 160 PHE cc_start: 0.8396 (m-80) cc_final: 0.8036 (m-80) REVERT: C 303 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8460 (t80) REVERT: C 423 LEU cc_start: 0.8971 (mp) cc_final: 0.8701 (mp) REVERT: C 799 MET cc_start: 0.7692 (tpp) cc_final: 0.7153 (tpt) REVERT: C 982 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7183 (pp) REVERT: C 1009 MET cc_start: 0.8174 (mmm) cc_final: 0.7886 (mmm) REVERT: B 353 LEU cc_start: 0.8296 (mt) cc_final: 0.7953 (tt) REVERT: B 806 ASN cc_start: 0.8797 (p0) cc_final: 0.8539 (p0) REVERT: D 145 TYR cc_start: 0.7245 (m-80) cc_final: 0.6550 (m-80) REVERT: D 303 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8493 (t80) REVERT: D 1004 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8347 (mm) outliers start: 118 outliers final: 95 residues processed: 441 average time/residue: 0.3070 time to fit residues: 227.8837 Evaluate side-chains 448 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 348 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 284 optimal weight: 0.2980 chunk 303 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27688 Z= 0.148 Angle : 0.584 12.612 37567 Z= 0.283 Chirality : 0.041 0.187 4302 Planarity : 0.004 0.055 4717 Dihedral : 4.232 54.576 3622 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.85 % Allowed : 34.31 % Favored : 61.84 % 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: -0.91 (0.15), residues: 3351 helix: 0.39 (0.14), residues: 1497 sheet: -1.17 (0.30), residues: 359 loop : -1.46 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 246 HIS 0.007 0.001 HIS A 350 PHE 0.024 0.001 PHE A 217 TYR 0.020 0.001 TYR C 279 ARG 0.005 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 359 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8139 (m-80) cc_final: 0.7387 (m-80) REVERT: A 321 GLU cc_start: 0.8747 (pm20) cc_final: 0.8508 (pm20) REVERT: A 354 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 374 GLU cc_start: 0.7757 (tp30) cc_final: 0.7348 (mm-30) REVERT: C 159 PHE cc_start: 0.8901 (t80) cc_final: 0.8028 (m-80) REVERT: C 160 PHE cc_start: 0.8333 (m-80) cc_final: 0.7987 (m-80) REVERT: C 188 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6998 (t80) REVERT: C 303 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8430 (t80) REVERT: C 423 LEU cc_start: 0.8890 (mp) cc_final: 0.8672 (mp) REVERT: C 799 MET cc_start: 0.7707 (tpp) cc_final: 0.7274 (tpp) REVERT: C 982 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7171 (pp) REVERT: C 1009 MET cc_start: 0.8167 (mmm) cc_final: 0.7863 (mmm) REVERT: B 224 LEU cc_start: 0.8250 (mt) cc_final: 0.7773 (tp) REVERT: B 303 PHE cc_start: 0.8882 (m-80) cc_final: 0.8650 (m-10) REVERT: B 353 LEU cc_start: 0.8284 (mt) cc_final: 0.7928 (tt) REVERT: B 558 PHE cc_start: 0.6930 (t80) cc_final: 0.6571 (t80) REVERT: B 806 ASN cc_start: 0.8828 (p0) cc_final: 0.8593 (p0) REVERT: B 1053 MET cc_start: 0.7557 (mmm) cc_final: 0.6875 (mmm) REVERT: D 145 TYR cc_start: 0.7257 (m-80) cc_final: 0.6560 (m-80) REVERT: D 303 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8490 (t80) REVERT: D 1004 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8381 (mm) outliers start: 115 outliers final: 100 residues processed: 440 average time/residue: 0.3184 time to fit residues: 236.3134 Evaluate side-chains 456 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 350 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 164 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27688 Z= 0.164 Angle : 0.596 13.332 37567 Z= 0.289 Chirality : 0.041 0.180 4302 Planarity : 0.004 0.055 4717 Dihedral : 4.136 51.949 3620 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.75 % Allowed : 34.48 % Favored : 61.77 % 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: -0.91 (0.15), residues: 3351 helix: 0.39 (0.14), residues: 1497 sheet: -1.18 (0.30), residues: 349 loop : -1.45 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 176 HIS 0.007 0.001 HIS A 350 PHE 0.025 0.001 PHE A 217 TYR 0.021 0.001 TYR C 279 ARG 0.007 0.000 ARG A 974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 354 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.8135 (m-80) cc_final: 0.7391 (m-80) REVERT: A 321 GLU cc_start: 0.8758 (pm20) cc_final: 0.8539 (pm20) REVERT: C 159 PHE cc_start: 0.8899 (t80) cc_final: 0.8031 (m-80) REVERT: C 160 PHE cc_start: 0.8336 (m-80) cc_final: 0.7991 (m-80) REVERT: C 188 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7011 (t80) REVERT: C 303 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8425 (t80) REVERT: C 423 LEU cc_start: 0.8899 (mp) cc_final: 0.8657 (mp) REVERT: C 799 MET cc_start: 0.7722 (tpp) cc_final: 0.7297 (tpp) REVERT: C 982 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7143 (pp) REVERT: C 1009 MET cc_start: 0.8174 (mmm) cc_final: 0.7867 (mmm) REVERT: B 224 LEU cc_start: 0.8224 (mt) cc_final: 0.7747 (tp) REVERT: B 303 PHE cc_start: 0.8901 (m-80) cc_final: 0.8698 (m-10) REVERT: B 353 LEU cc_start: 0.8251 (mt) cc_final: 0.7895 (tt) REVERT: B 393 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7725 (ptp90) REVERT: B 558 PHE cc_start: 0.6937 (t80) cc_final: 0.6711 (t80) REVERT: B 806 ASN cc_start: 0.8821 (p0) cc_final: 0.8587 (p0) REVERT: B 1009 MET cc_start: 0.8630 (pmm) cc_final: 0.8370 (pmm) REVERT: D 303 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8489 (t80) REVERT: D 1004 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8340 (mm) outliers start: 112 outliers final: 101 residues processed: 432 average time/residue: 0.3188 time to fit residues: 232.8062 Evaluate side-chains 453 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 347 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 808 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 746 PHE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1052 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 275 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN D 402 GLN ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101239 restraints weight = 138026.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102749 restraints weight = 60257.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104097 restraints weight = 42015.944| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27688 Z= 0.204 Angle : 0.615 13.853 37567 Z= 0.299 Chirality : 0.042 0.181 4302 Planarity : 0.004 0.055 4717 Dihedral : 4.193 51.895 3620 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.85 % Allowed : 34.65 % Favored : 61.51 % 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: -0.94 (0.15), residues: 3351 helix: 0.36 (0.14), residues: 1496 sheet: -1.22 (0.30), residues: 349 loop : -1.45 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 246 HIS 0.007 0.001 HIS A 350 PHE 0.029 0.001 PHE B 391 TYR 0.021 0.001 TYR C 279 ARG 0.017 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5510.37 seconds wall clock time: 100 minutes 25.04 seconds (6025.04 seconds total)