Starting phenix.real_space_refine on Mon Mar 25 00:25:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s63_24848/03_2024/7s63_24848.pdb" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 220 5.16 5 C 28704 2.51 5 N 7292 2.21 5 O 8992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A TYR 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1261": "OD1" <-> "OD2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 910": "OD1" <-> "OD2" Residue "B TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1020": "OD1" <-> "OD2" Residue "B TYR 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1261": "OD1" <-> "OD2" Residue "B TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 570": "OD1" <-> "OD2" Residue "C TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "C PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1384": "OE1" <-> "OE2" Residue "C PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D GLU 662": "OE1" <-> "OE2" Residue "D GLU 691": "OE1" <-> "OE2" Residue "D GLU 703": "OE1" <-> "OE2" Residue "D PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 974": "OE1" <-> "OE2" Residue "D TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1020": "OD1" <-> "OD2" Residue "D TYR 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1261": "OD1" <-> "OD2" Residue "D PHE 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1384": "OE1" <-> "OE2" Residue "D PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45208 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 22.60, per 1000 atoms: 0.50 Number of scatterers: 45208 At special positions: 0 Unit cell: (219.03, 230.79, 142.59, 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 220 16.00 O 8992 8.00 N 7292 7.00 C 28704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 283 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 640 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A1327 " - pdb=" SG CYS A1441 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 283 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 640 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B1327 " - pdb=" SG CYS B1441 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 283 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 559 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 640 " - pdb=" SG CYS C 688 " distance=2.03 Simple disulfide: pdb=" SG CYS C 809 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C1327 " - pdb=" SG CYS C1441 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 262 " - pdb=" SG CYS D 283 " distance=2.04 Simple disulfide: pdb=" SG CYS D 467 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS D 591 " - pdb=" SG CYS D 758 " distance=2.03 Simple disulfide: pdb=" SG CYS D 640 " - pdb=" SG CYS D 688 " distance=2.03 Simple disulfide: pdb=" SG CYS D 809 " - pdb=" SG CYS D 836 " distance=2.03 Simple disulfide: pdb=" SG CYS D1327 " - pdb=" SG CYS D1441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied NAG-ASN " NAG A2101 " - " ASN A 64 " " NAG A2102 " - " ASN A 81 " " NAG A2103 " - " ASN A 242 " " NAG A2104 " - " ASN A 285 " " NAG A2105 " - " ASN A 415 " " NAG A2106 " - " ASN A 472 " " NAG A2107 " - " ASN A 526 " " NAG A2108 " - " ASN A 578 " " NAG A2109 " - " ASN A 721 " " NAG A2110 " - " ASN A 773 " " NAG A2111 " - " ASN A 918 " " NAG A2112 " - " ASN A 977 " " NAG A2113 " - " ASN A1096 " " NAG A2114 " - " ASN A1266 " " NAG A2115 " - " ASN A1286 " " NAG A2116 " - " ASN A1292 " " NAG A2117 " - " ASN A1348 " " NAG B2101 " - " ASN B 64 " " NAG B2102 " - " ASN B 81 " " NAG B2103 " - " ASN B 242 " " NAG B2104 " - " ASN B 285 " " NAG B2105 " - " ASN B 415 " " NAG B2106 " - " ASN B 472 " " NAG B2107 " - " ASN B 526 " " NAG B2108 " - " ASN B 578 " " NAG B2109 " - " ASN B 721 " " NAG B2110 " - " ASN B 773 " " NAG B2111 " - " ASN B 918 " " NAG B2112 " - " ASN B 977 " " NAG B2113 " - " ASN B1096 " " NAG B2114 " - " ASN B1266 " " NAG B2115 " - " ASN B1286 " " NAG B2116 " - " ASN B1292 " " NAG B2117 " - " ASN B1348 " " NAG C2101 " - " ASN C 64 " " NAG C2102 " - " ASN C 81 " " NAG C2103 " - " ASN C 242 " " NAG C2104 " - " ASN C 285 " " NAG C2105 " - " ASN C 415 " " NAG C2106 " - " ASN C 472 " " NAG C2107 " - " ASN C 526 " " NAG C2108 " - " ASN C 578 " " NAG C2109 " - " ASN C 721 " " NAG C2110 " - " ASN C 773 " " NAG C2111 " - " ASN C 918 " " NAG C2112 " - " ASN C 977 " " NAG C2113 " - " ASN C1096 " " NAG C2114 " - " ASN C1266 " " NAG C2115 " - " ASN C1286 " " NAG C2116 " - " ASN C1292 " " NAG C2117 " - " ASN C1348 " " NAG D2101 " - " ASN D 64 " " NAG D2102 " - " ASN D 81 " " NAG D2103 " - " ASN D 242 " " NAG D2104 " - " ASN D 285 " " NAG D2105 " - " ASN D 415 " " NAG D2106 " - " ASN D 472 " " NAG D2107 " - " ASN D 526 " " NAG D2108 " - " ASN D 578 " " NAG D2109 " - " ASN D 721 " " NAG D2110 " - " ASN D 773 " " NAG D2111 " - " ASN D 918 " " NAG D2112 " - " ASN D 977 " " NAG D2113 " - " ASN D1096 " " NAG D2114 " - " ASN D1266 " " NAG D2115 " - " ASN D1286 " " NAG D2116 " - " ASN D1292 " " NAG D2117 " - " ASN D1348 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.41 Conformation dependent library (CDL) restraints added in 7.6 seconds 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10576 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 108 sheets defined 15.6% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.714A pdb=" N LEU A 600 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 942 through 946 removed outlier: 3.577A pdb=" N LEU A 945 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 946 " --> pdb=" O LEU A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 947 through 951 removed outlier: 4.008A pdb=" N LEU A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 967 through 979 removed outlier: 4.520A pdb=" N TYR A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1002 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1043 through 1057 removed outlier: 3.554A pdb=" N GLN A1047 " --> pdb=" O ASP A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1095 Processing helix chain 'A' and resid 1101 through 1113 removed outlier: 3.546A pdb=" N ALA A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1134 Processing helix chain 'A' and resid 1138 through 1150 removed outlier: 3.600A pdb=" N SER A1149 " --> pdb=" O ASN A1145 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1195 removed outlier: 4.326A pdb=" N VAL A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1185 " --> pdb=" O ALA A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1217 removed outlier: 3.999A pdb=" N THR A1205 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A1213 " --> pdb=" O GLN A1209 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A1217 " --> pdb=" O TRP A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1243 removed outlier: 3.890A pdb=" N VAL A1232 " --> pdb=" O GLN A1228 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1243 " --> pdb=" O PHE A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1376 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.791A pdb=" N LEU B 600 " --> pdb=" O ASP B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 942 through 946 removed outlier: 3.615A pdb=" N LEU B 945 " --> pdb=" O GLY B 942 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 946 " --> pdb=" O LEU B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 946' Processing helix chain 'B' and resid 958 through 963 Processing helix chain 'B' and resid 967 through 979 removed outlier: 4.415A pdb=" N TYR B 971 " --> pdb=" O ALA B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1003 removed outlier: 3.853A pdb=" N ARG B1003 " --> pdb=" O TYR B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1037 Processing helix chain 'B' and resid 1043 through 1057 removed outlier: 3.648A pdb=" N GLN B1047 " --> pdb=" O ASP B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1095 Processing helix chain 'B' and resid 1101 through 1113 removed outlier: 3.634A pdb=" N ALA B1113 " --> pdb=" O GLY B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1134 removed outlier: 3.779A pdb=" N TYR B1126 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1150 removed outlier: 3.624A pdb=" N SER B1149 " --> pdb=" O ASN B1145 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1195 removed outlier: 4.366A pdb=" N VAL B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B1184 " --> pdb=" O PRO B1180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B1185 " --> pdb=" O ALA B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1217 removed outlier: 3.862A pdb=" N THR B1205 " --> pdb=" O HIS B1201 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR B1206 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B1213 " --> pdb=" O GLN B1209 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B1214 " --> pdb=" O ILE B1210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B1217 " --> pdb=" O TRP B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1243 removed outlier: 3.915A pdb=" N VAL B1232 " --> pdb=" O GLN B1228 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B1243 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1376 Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.779A pdb=" N LEU C 600 " --> pdb=" O ASP C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 617 Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 939 through 946 removed outlier: 4.438A pdb=" N LEU C 943 " --> pdb=" O VAL C 940 " (cutoff:3.500A) Proline residue: C 944 - end of helix Processing helix chain 'C' and resid 947 through 951 removed outlier: 4.183A pdb=" N LEU C 951 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 963 Processing helix chain 'C' and resid 967 through 979 removed outlier: 4.542A pdb=" N TYR C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1002 Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'C' and resid 1022 through 1037 Processing helix chain 'C' and resid 1043 through 1057 Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1095 Processing helix chain 'C' and resid 1101 through 1113 removed outlier: 3.748A pdb=" N ALA C1113 " --> pdb=" O GLY C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1134 removed outlier: 3.524A pdb=" N TYR C1126 " --> pdb=" O TYR C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 3.559A pdb=" N SER C1149 " --> pdb=" O ASN C1145 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C1150 " --> pdb=" O GLU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1195 removed outlier: 4.360A pdb=" N VAL C1183 " --> pdb=" O SER C1179 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C1184 " --> pdb=" O PRO C1180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C1185 " --> pdb=" O ALA C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1217 removed outlier: 4.038A pdb=" N THR C1205 " --> pdb=" O HIS C1201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C1213 " --> pdb=" O GLN C1209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C1217 " --> pdb=" O TRP C1213 " (cutoff:3.500A) Processing helix chain 'C' and resid 1226 through 1243 removed outlier: 4.036A pdb=" N VAL C1232 " --> pdb=" O GLN C1228 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C1243 " --> pdb=" O PHE C1239 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1376 Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.803A pdb=" N LEU D 600 " --> pdb=" O ASP D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 664 through 669 Processing helix chain 'D' and resid 942 through 946 removed outlier: 3.613A pdb=" N LEU D 945 " --> pdb=" O GLY D 942 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 946 " --> pdb=" O LEU D 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 946' Processing helix chain 'D' and resid 958 through 963 Processing helix chain 'D' and resid 967 through 979 removed outlier: 4.457A pdb=" N TYR D 971 " --> pdb=" O ALA D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 1003 removed outlier: 3.870A pdb=" N ARG D1003 " --> pdb=" O TYR D 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1037 Processing helix chain 'D' and resid 1043 through 1057 removed outlier: 3.656A pdb=" N GLN D1047 " --> pdb=" O ASP D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1095 Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.605A pdb=" N ALA D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1134 removed outlier: 3.555A pdb=" N TYR D1126 " --> pdb=" O TYR D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1148 Processing helix chain 'D' and resid 1179 through 1195 removed outlier: 4.375A pdb=" N VAL D1183 " --> pdb=" O SER D1179 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D1184 " --> pdb=" O PRO D1180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D1185 " --> pdb=" O ALA D1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1217 removed outlier: 3.886A pdb=" N THR D1205 " --> pdb=" O HIS D1201 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR D1206 " --> pdb=" O ASP D1202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D1213 " --> pdb=" O GLN D1209 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D1214 " --> pdb=" O ILE D1210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D1217 " --> pdb=" O TRP D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.887A pdb=" N VAL D1232 " --> pdb=" O GLN D1228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D1243 " --> pdb=" O PHE D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1376 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 8.896A pdb=" N ARG A 40 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 29 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.607A pdb=" N LEU A 33 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 95 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.107A pdb=" N VAL A 158 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.579A pdb=" N THR A 284 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 261 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 256 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.586A pdb=" N ASN A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 348 Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB5, first strand: chain 'A' and resid 454 through 458 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB7, first strand: chain 'A' and resid 503 through 512 removed outlier: 4.880A pdb=" N GLN A 505 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 497 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A 492 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE A 542 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB9, first strand: chain 'A' and resid 590 through 596 Processing sheet with id=AC1, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AC2, first strand: chain 'A' and resid 780 through 785 removed outlier: 3.745A pdb=" N SER A 785 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A 799 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 846 " --> pdb=" O ILE A 825 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 780 through 785 removed outlier: 3.745A pdb=" N SER A 785 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A 799 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 839 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.358A pdb=" N LEU A 790 " --> pdb=" O GLN A 892 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 810 through 811 Processing sheet with id=AC6, first strand: chain 'A' and resid 896 through 909 removed outlier: 3.547A pdb=" N VAL A 908 " --> pdb=" O GLY A1295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A1295 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A1263 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 896 through 909 removed outlier: 3.547A pdb=" N VAL A 908 " --> pdb=" O GLY A1295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A1295 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A1298 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 937 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1152 through 1153 Processing sheet with id=AC9, first strand: chain 'A' and resid 1318 through 1324 removed outlier: 3.675A pdb=" N GLN A1364 " --> pdb=" O LEU A1408 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1381 through 1385 removed outlier: 3.721A pdb=" N LYS A1381 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A1420 " --> pdb=" O GLN A1358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 77 through 84 removed outlier: 8.923A pdb=" N ARG B 40 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 29 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.658A pdb=" N LEU B 33 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 95 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AD5, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=AD6, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AD7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'B' and resid 170 through 171 removed outlier: 3.976A pdb=" N VAL B 158 " --> pdb=" O TRP B 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AE1, first strand: chain 'B' and resid 284 through 290 removed outlier: 3.553A pdb=" N THR B 284 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 261 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 290 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 255 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 256 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AE3, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AE4, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AE5, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AE6, first strand: chain 'B' and resid 454 through 459 removed outlier: 4.456A pdb=" N SER B 474 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE8, first strand: chain 'B' and resid 507 through 512 removed outlier: 6.877A pdb=" N THR B 492 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 542 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AF1, first strand: chain 'B' and resid 572 through 573 removed outlier: 3.524A pdb=" N GLY B 573 " --> pdb=" O THR B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 590 through 596 Processing sheet with id=AF3, first strand: chain 'B' and resid 780 through 785 removed outlier: 3.754A pdb=" N SER B 785 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 799 " --> pdb=" O SER B 785 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 846 " --> pdb=" O ILE B 825 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 780 through 785 removed outlier: 3.754A pdb=" N SER B 785 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 799 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 789 through 791 removed outlier: 6.294A pdb=" N LEU B 790 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 896 through 909 Processing sheet with id=AF7, first strand: chain 'B' and resid 896 through 909 removed outlier: 4.210A pdb=" N LEU B1298 " --> pdb=" O VAL B 937 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 937 " --> pdb=" O LEU B1298 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1152 through 1153 Processing sheet with id=AF9, first strand: chain 'B' and resid 1318 through 1324 removed outlier: 3.911A pdb=" N GLN B1364 " --> pdb=" O LEU B1408 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1381 through 1385 removed outlier: 3.650A pdb=" N LYS B1381 " --> pdb=" O TYR B1392 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B1420 " --> pdb=" O GLN B1358 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 77 through 84 removed outlier: 8.950A pdb=" N ARG C 40 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 29 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.555A pdb=" N LEU C 33 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 95 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AG5, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AG6, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AG7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AG8, first strand: chain 'C' and resid 170 through 171 removed outlier: 4.125A pdb=" N VAL C 158 " --> pdb=" O TRP C 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AH1, first strand: chain 'C' and resid 232 through 233 removed outlier: 3.782A pdb=" N SER C 256 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 261 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 284 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.580A pdb=" N ASN C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 344 through 348 Processing sheet with id=AH4, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AH5, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AH6, first strand: chain 'C' and resid 454 through 459 removed outlier: 4.458A pdb=" N SER C 474 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AH8, first strand: chain 'C' and resid 503 through 512 removed outlier: 4.913A pdb=" N GLN C 505 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 497 " --> pdb=" O GLN C 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR C 492 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE C 542 " --> pdb=" O THR C 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AI1, first strand: chain 'C' and resid 590 through 596 Processing sheet with id=AI2, first strand: chain 'C' and resid 647 through 648 Processing sheet with id=AI3, first strand: chain 'C' and resid 780 through 785 removed outlier: 3.761A pdb=" N SER C 785 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 799 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 846 " --> pdb=" O ILE C 825 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 780 through 785 removed outlier: 3.761A pdb=" N SER C 785 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 799 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 839 " --> pdb=" O ASN C 804 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 789 through 791 removed outlier: 6.337A pdb=" N LEU C 790 " --> pdb=" O GLN C 892 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 815 " --> pdb=" O SER C 860 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 896 through 909 removed outlier: 3.568A pdb=" N VAL C 908 " --> pdb=" O GLY C1295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1295 " --> pdb=" O VAL C 908 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C1257 " --> pdb=" O ASP C1261 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP C1261 " --> pdb=" O SER C1257 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 896 through 909 removed outlier: 3.568A pdb=" N VAL C 908 " --> pdb=" O GLY C1295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1295 " --> pdb=" O VAL C 908 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C1298 " --> pdb=" O VAL C 937 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 937 " --> pdb=" O LEU C1298 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 1152 through 1153 Processing sheet with id=AI9, first strand: chain 'C' and resid 1318 through 1324 removed outlier: 3.906A pdb=" N GLN C1364 " --> pdb=" O LEU C1408 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 1381 through 1385 removed outlier: 3.797A pdb=" N LYS C1381 " --> pdb=" O TYR C1392 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1420 " --> pdb=" O GLN C1358 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 77 through 84 removed outlier: 8.817A pdb=" N ARG D 40 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 29 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.670A pdb=" N LEU D 33 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 95 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AJ5, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=AJ6, first strand: chain 'D' and resid 136 through 138 Processing sheet with id=AJ7, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AJ8, first strand: chain 'D' and resid 170 through 171 removed outlier: 4.109A pdb=" N VAL D 158 " --> pdb=" O TRP D 171 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 223 through 225 Processing sheet with id=AK1, first strand: chain 'D' and resid 284 through 290 removed outlier: 3.573A pdb=" N THR D 284 " --> pdb=" O CYS D 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS D 261 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 290 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY D 255 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D 256 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 344 through 348 removed outlier: 3.530A pdb=" N ASN D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 344 through 348 Processing sheet with id=AK4, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AK5, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AK6, first strand: chain 'D' and resid 454 through 459 removed outlier: 4.467A pdb=" N SER D 474 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AK8, first strand: chain 'D' and resid 507 through 512 removed outlier: 7.087A pdb=" N THR D 492 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE D 542 " --> pdb=" O THR D 492 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 567 through 568 Processing sheet with id=AL1, first strand: chain 'D' and resid 590 through 596 Processing sheet with id=AL2, first strand: chain 'D' and resid 780 through 785 removed outlier: 3.797A pdb=" N SER D 785 " --> pdb=" O LYS D 799 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 799 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 845 " --> pdb=" O MET D 798 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN D 846 " --> pdb=" O ILE D 825 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 780 through 785 removed outlier: 3.797A pdb=" N SER D 785 " --> pdb=" O LYS D 799 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 799 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 839 " --> pdb=" O ASN D 804 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'D' and resid 789 through 791 removed outlier: 6.307A pdb=" N LEU D 790 " --> pdb=" O GLN D 892 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'D' and resid 896 through 909 removed outlier: 3.507A pdb=" N GLY D1263 " --> pdb=" O LEU D1255 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'D' and resid 896 through 909 removed outlier: 4.157A pdb=" N LEU D1298 " --> pdb=" O VAL D 937 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 937 " --> pdb=" O LEU D1298 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'D' and resid 1152 through 1153 Processing sheet with id=AL8, first strand: chain 'D' and resid 1318 through 1324 removed outlier: 3.889A pdb=" N GLN D1364 " --> pdb=" O LEU D1408 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'D' and resid 1381 through 1385 removed outlier: 3.668A pdb=" N LYS D1381 " --> pdb=" O TYR D1392 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER D1420 " --> pdb=" O GLN D1358 " (cutoff:3.500A) 1571 hydrogen bonds defined for protein. 4266 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: 26.37 Time building geometry restraints manager: 17.70 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: 14509 1.34 - 1.47: 11128 1.47 - 1.59: 20194 1.59 - 1.71: 1 1.71 - 1.83: 312 Bond restraints: 46144 Sorted by residual: bond pdb=" C1 NAG C2103 " pdb=" O5 NAG C2103 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG B2103 " pdb=" O5 NAG B2103 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG D2103 " pdb=" O5 NAG D2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG B2109 " pdb=" O5 NAG B2109 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 46139 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.25: 811 105.25 - 112.47: 23809 112.47 - 119.69: 15048 119.69 - 126.91: 22670 126.91 - 134.13: 398 Bond angle restraints: 62736 Sorted by residual: angle pdb=" CA PRO A 916 " pdb=" N PRO A 916 " pdb=" CD PRO A 916 " ideal model delta sigma weight residual 112.00 99.51 12.49 1.40e+00 5.10e-01 7.96e+01 angle pdb=" C GLN B 73 " pdb=" N PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 125.00 100.34 24.66 4.10e+00 5.95e-02 3.62e+01 angle pdb=" C GLN A 73 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 125.00 100.65 24.35 4.10e+00 5.95e-02 3.53e+01 angle pdb=" C GLN D 73 " pdb=" N PRO D 74 " pdb=" CD PRO D 74 " ideal model delta sigma weight residual 125.00 100.82 24.18 4.10e+00 5.95e-02 3.48e+01 angle pdb=" C ARG C 271 " pdb=" CA ARG C 271 " pdb=" CB ARG C 271 " ideal model delta sigma weight residual 116.54 109.87 6.67 1.15e+00 7.56e-01 3.37e+01 ... (remaining 62731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 26304 23.90 - 47.80: 1659 47.80 - 71.71: 339 71.71 - 95.61: 118 95.61 - 119.51: 124 Dihedral angle restraints: 28544 sinusoidal: 11992 harmonic: 16552 Sorted by residual: dihedral pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " pdb=" SG CYS B 688 " pdb=" CB CYS B 688 " ideal model delta sinusoidal sigma weight residual -86.00 -174.82 88.82 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS A 640 " pdb=" SG CYS A 640 " pdb=" SG CYS A 688 " pdb=" CB CYS A 688 " ideal model delta sinusoidal sigma weight residual -86.00 -174.16 88.16 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS D 640 " pdb=" SG CYS D 640 " pdb=" SG CYS D 688 " pdb=" CB CYS D 688 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 28541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 7165 0.120 - 0.239: 164 0.239 - 0.359: 10 0.359 - 0.478: 0 0.478 - 0.598: 1 Chirality restraints: 7340 Sorted by residual: chirality pdb=" C1 NAG D2102 " pdb=" ND2 ASN D 81 " pdb=" C2 NAG D2102 " pdb=" O5 NAG D2102 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" C1 NAG D2108 " pdb=" ND2 ASN D 578 " pdb=" C2 NAG D2108 " pdb=" O5 NAG D2108 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG B2108 " pdb=" ND2 ASN B 578 " pdb=" C2 NAG B2108 " pdb=" O5 NAG B2108 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 7337 not shown) Planarity restraints: 8072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 73 " -0.127 5.00e-02 4.00e+02 1.91e-01 5.84e+01 pdb=" N PRO B 74 " 0.330 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " -0.117 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 73 " -0.126 5.00e-02 4.00e+02 1.90e-01 5.75e+01 pdb=" N PRO D 74 " 0.327 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 73 " 0.125 5.00e-02 4.00e+02 1.89e-01 5.71e+01 pdb=" N PRO A 74 " -0.326 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.086 5.00e-02 4.00e+02 ... (remaining 8069 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 78 2.34 - 2.98: 22947 2.98 - 3.62: 65409 3.62 - 4.26: 94855 4.26 - 4.90: 158468 Nonbonded interactions: 341757 Sorted by model distance: nonbonded pdb=" SG CYS C 958 " pdb=" CD GLN C 961 " model vdw 1.697 3.630 nonbonded pdb=" SG CYS D 958 " pdb=" CD GLN D 961 " model vdw 1.697 3.630 nonbonded pdb=" SG CYS A 958 " pdb=" CD GLN A 961 " model vdw 1.698 3.630 nonbonded pdb=" SG CYS B 958 " pdb=" CD GLN B 961 " model vdw 1.698 3.630 nonbonded pdb=" SG CYS A 958 " pdb=" CG GLN A 961 " model vdw 1.919 3.800 ... (remaining 341752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.910 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: 0.030 Extract box with map and model: 6.320 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 118.750 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 0.120 46144 Z= 0.278 Angle : 0.789 24.661 62736 Z= 0.419 Chirality : 0.050 0.598 7340 Planarity : 0.007 0.191 8004 Dihedral : 18.502 119.512 17872 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.77 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.90 (0.11), residues: 5672 helix: 0.89 (0.18), residues: 804 sheet: -0.54 (0.12), residues: 1952 loop : -2.50 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B1015 HIS 0.003 0.001 HIS A 76 PHE 0.026 0.002 PHE A1030 TYR 0.035 0.002 TYR C 653 ARG 0.013 0.001 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6334 (m-80) cc_final: 0.5086 (m-80) REVERT: A 446 MET cc_start: 0.8496 (mmm) cc_final: 0.8116 (mmm) REVERT: A 478 ILE cc_start: 0.8883 (tp) cc_final: 0.8644 (tt) REVERT: A 1337 ILE cc_start: 0.7541 (mt) cc_final: 0.7245 (mt) REVERT: B 430 TYR cc_start: 0.8144 (t80) cc_final: 0.7895 (t80) REVERT: B 446 MET cc_start: 0.8143 (mmm) cc_final: 0.7861 (mmm) REVERT: C 451 GLU cc_start: 0.7088 (pp20) cc_final: 0.6809 (pp20) REVERT: C 1337 ILE cc_start: 0.8102 (mt) cc_final: 0.7678 (mt) REVERT: D 277 LYS cc_start: 0.4640 (ptpp) cc_final: 0.3931 (ptpp) REVERT: D 430 TYR cc_start: 0.8006 (t80) cc_final: 0.7757 (t80) REVERT: D 446 MET cc_start: 0.8231 (mmm) cc_final: 0.7998 (mmm) REVERT: D 478 ILE cc_start: 0.8797 (tp) cc_final: 0.8458 (tt) REVERT: D 484 MET cc_start: 0.7556 (ppp) cc_final: 0.6839 (ppp) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.5200 time to fit residues: 413.1276 Evaluate side-chains 364 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 479 optimal weight: 0.9980 chunk 430 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 445 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 chunk 331 optimal weight: 0.6980 chunk 515 optimal weight: 20.0000 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN A1415 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 375 ASN C 949 GLN C1047 GLN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 375 ASN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN D1235 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 46144 Z= 0.330 Angle : 0.715 10.919 62736 Z= 0.355 Chirality : 0.050 0.416 7340 Planarity : 0.006 0.139 8004 Dihedral : 13.953 108.268 7592 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.75 % Favored : 89.03 % Rotamer: Outliers : 0.10 % Allowed : 7.23 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.87 (0.11), residues: 5672 helix: 1.02 (0.18), residues: 812 sheet: -0.43 (0.12), residues: 1888 loop : -2.55 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 433 HIS 0.005 0.001 HIS B 443 PHE 0.020 0.002 PHE D 448 TYR 0.029 0.002 TYR D 540 ARG 0.010 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 436 time to evaluate : 5.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6364 (m-80) cc_final: 0.5299 (m-80) REVERT: A 750 THR cc_start: 0.6660 (p) cc_final: 0.6452 (p) REVERT: A 1337 ILE cc_start: 0.7615 (mt) cc_final: 0.7326 (mt) REVERT: B 430 TYR cc_start: 0.8261 (t80) cc_final: 0.7938 (t80) REVERT: B 446 MET cc_start: 0.8083 (mmm) cc_final: 0.7832 (mmm) REVERT: C 74 PRO cc_start: 0.6693 (OUTLIER) cc_final: 0.6474 (Cg_endo) REVERT: C 430 TYR cc_start: 0.8270 (t80) cc_final: 0.8008 (t80) REVERT: C 446 MET cc_start: 0.8428 (mmm) cc_final: 0.8114 (mmm) REVERT: C 451 GLU cc_start: 0.7563 (pp20) cc_final: 0.7209 (pp20) REVERT: C 1337 ILE cc_start: 0.8132 (mt) cc_final: 0.7714 (mt) REVERT: D 277 LYS cc_start: 0.4765 (ptpp) cc_final: 0.3699 (ptpp) REVERT: D 430 TYR cc_start: 0.8363 (t80) cc_final: 0.8034 (t80) REVERT: D 478 ILE cc_start: 0.8857 (tp) cc_final: 0.8651 (tt) REVERT: D 484 MET cc_start: 0.7278 (ppp) cc_final: 0.6983 (ppp) outliers start: 5 outliers final: 1 residues processed: 441 average time/residue: 0.5348 time to fit residues: 400.6985 Evaluate side-chains 349 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 286 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 429 optimal weight: 0.8980 chunk 351 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 516 optimal weight: 40.0000 chunk 558 optimal weight: 6.9990 chunk 460 optimal weight: 0.9980 chunk 512 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 414 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 274 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46144 Z= 0.239 Angle : 0.686 14.110 62736 Z= 0.335 Chirality : 0.049 0.598 7340 Planarity : 0.006 0.151 8004 Dihedral : 10.954 107.143 7592 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.05 % Favored : 89.74 % Rotamer: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.83 (0.11), residues: 5672 helix: 1.08 (0.18), residues: 812 sheet: -0.32 (0.13), residues: 1852 loop : -2.57 (0.10), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 433 HIS 0.005 0.001 HIS B 506 PHE 0.015 0.002 PHE D1254 TYR 0.046 0.001 TYR A 268 ARG 0.006 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6222 (m-80) cc_final: 0.5193 (m-80) REVERT: A 430 TYR cc_start: 0.7940 (t80) cc_final: 0.7616 (t80) REVERT: A 750 THR cc_start: 0.6683 (p) cc_final: 0.6433 (p) REVERT: A 822 PHE cc_start: 0.4969 (p90) cc_final: 0.4227 (p90) REVERT: A 1337 ILE cc_start: 0.7630 (mt) cc_final: 0.7327 (mt) REVERT: B 282 ILE cc_start: 0.8044 (tt) cc_final: 0.7829 (tt) REVERT: B 430 TYR cc_start: 0.8242 (t80) cc_final: 0.7884 (t80) REVERT: B 446 MET cc_start: 0.8125 (mmm) cc_final: 0.7829 (mmm) REVERT: B 1375 ASN cc_start: 0.7357 (p0) cc_final: 0.7077 (p0) REVERT: C 430 TYR cc_start: 0.8170 (t80) cc_final: 0.7923 (t80) REVERT: C 446 MET cc_start: 0.8368 (mmm) cc_final: 0.8110 (mmm) REVERT: C 451 GLU cc_start: 0.7362 (pp20) cc_final: 0.7001 (pp20) REVERT: C 1337 ILE cc_start: 0.8226 (mt) cc_final: 0.7951 (mt) REVERT: D 430 TYR cc_start: 0.8334 (t80) cc_final: 0.8019 (t80) REVERT: D 433 TRP cc_start: 0.7211 (p-90) cc_final: 0.6949 (p-90) REVERT: D 778 LEU cc_start: 0.7858 (tt) cc_final: 0.7637 (tt) REVERT: D 1001 GLN cc_start: 0.5694 (tm-30) cc_final: 0.5427 (tm-30) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.5262 time to fit residues: 414.4687 Evaluate side-chains 357 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 510 optimal weight: 40.0000 chunk 388 optimal weight: 6.9990 chunk 268 optimal weight: 0.0050 chunk 57 optimal weight: 0.4980 chunk 246 optimal weight: 40.0000 chunk 346 optimal weight: 0.0050 chunk 518 optimal weight: 20.0000 chunk 549 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 491 optimal weight: 2.9990 chunk 147 optimal weight: 0.0010 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A1235 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46144 Z= 0.167 Angle : 0.640 15.956 62736 Z= 0.312 Chirality : 0.048 0.370 7340 Planarity : 0.005 0.158 8004 Dihedral : 9.271 106.627 7592 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.45 % Favored : 90.37 % Rotamer: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.76 (0.11), residues: 5672 helix: 1.04 (0.18), residues: 800 sheet: -0.32 (0.12), residues: 1932 loop : -2.50 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 433 HIS 0.004 0.001 HIS D 506 PHE 0.018 0.001 PHE C 83 TYR 0.027 0.001 TYR A 268 ARG 0.008 0.000 ARG D1074 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6080 (m-80) cc_final: 0.5072 (m-80) REVERT: A 457 ASP cc_start: 0.8258 (t0) cc_final: 0.7863 (t0) REVERT: A 822 PHE cc_start: 0.4783 (p90) cc_final: 0.4079 (p90) REVERT: A 1337 ILE cc_start: 0.7489 (mt) cc_final: 0.7007 (mt) REVERT: B 282 ILE cc_start: 0.7808 (tt) cc_final: 0.7592 (tt) REVERT: B 430 TYR cc_start: 0.8199 (t80) cc_final: 0.7813 (t80) REVERT: B 446 MET cc_start: 0.8005 (mmm) cc_final: 0.7649 (mmm) REVERT: B 484 MET cc_start: 0.6671 (ppp) cc_final: 0.5846 (ppp) REVERT: B 822 PHE cc_start: 0.5184 (p90) cc_final: 0.4785 (p90) REVERT: B 1375 ASN cc_start: 0.7380 (p0) cc_final: 0.7177 (p0) REVERT: C 131 TYR cc_start: 0.6140 (m-80) cc_final: 0.5234 (m-80) REVERT: C 162 ASP cc_start: 0.6528 (p0) cc_final: 0.6257 (p0) REVERT: C 451 GLU cc_start: 0.6698 (pp20) cc_final: 0.6317 (pp20) REVERT: C 457 ASP cc_start: 0.8203 (t0) cc_final: 0.7971 (t0) REVERT: C 1337 ILE cc_start: 0.7723 (mt) cc_final: 0.7387 (mt) REVERT: D 430 TYR cc_start: 0.8307 (t80) cc_final: 0.7816 (t80) REVERT: D 433 TRP cc_start: 0.7192 (p-90) cc_final: 0.6907 (p-90) REVERT: D 1175 TYR cc_start: 0.6149 (t80) cc_final: 0.5824 (t80) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.5207 time to fit residues: 435.7699 Evaluate side-chains 346 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 457 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 408 optimal weight: 20.0000 chunk 226 optimal weight: 40.0000 chunk 468 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 chunk 492 optimal weight: 0.1980 chunk 138 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A1049 GLN A1235 GLN A1264 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 GLN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 817 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN D1264 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 46144 Z= 0.327 Angle : 0.700 13.991 62736 Z= 0.349 Chirality : 0.050 0.710 7340 Planarity : 0.006 0.148 8004 Dihedral : 9.095 105.093 7592 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.74 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.84 (0.11), residues: 5672 helix: 1.04 (0.18), residues: 808 sheet: -0.36 (0.12), residues: 1920 loop : -2.59 (0.10), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 433 HIS 0.005 0.001 HIS D 443 PHE 0.020 0.002 PHE C 448 TYR 0.031 0.002 TYR B 540 ARG 0.009 0.001 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 5.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6065 (m-80) cc_final: 0.5131 (m-80) REVERT: A 430 TYR cc_start: 0.8069 (t80) cc_final: 0.7771 (t80) REVERT: A 822 PHE cc_start: 0.4992 (p90) cc_final: 0.4593 (p90) REVERT: A 1245 PHE cc_start: 0.6669 (t80) cc_final: 0.6465 (t80) REVERT: B 282 ILE cc_start: 0.7992 (tt) cc_final: 0.7725 (tt) REVERT: B 430 TYR cc_start: 0.8373 (t80) cc_final: 0.7839 (t80) REVERT: B 822 PHE cc_start: 0.5224 (p90) cc_final: 0.5001 (p90) REVERT: B 999 TYR cc_start: 0.7236 (m-80) cc_final: 0.7029 (m-10) REVERT: C 430 TYR cc_start: 0.8103 (t80) cc_final: 0.7764 (t80) REVERT: C 446 MET cc_start: 0.8337 (mmm) cc_final: 0.8106 (mmm) REVERT: C 451 GLU cc_start: 0.7399 (pp20) cc_final: 0.7031 (pp20) REVERT: C 822 PHE cc_start: 0.5106 (p90) cc_final: 0.4430 (p90) REVERT: C 1337 ILE cc_start: 0.8013 (mt) cc_final: 0.7698 (mt) REVERT: D 430 TYR cc_start: 0.8412 (t80) cc_final: 0.7986 (t80) REVERT: D 433 TRP cc_start: 0.7316 (p-90) cc_final: 0.7063 (p-90) REVERT: D 1175 TYR cc_start: 0.6269 (t80) cc_final: 0.5965 (t80) REVERT: D 1375 ASN cc_start: 0.7209 (p0) cc_final: 0.6964 (p0) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.5158 time to fit residues: 397.8472 Evaluate side-chains 336 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 184 optimal weight: 0.9980 chunk 494 optimal weight: 0.9990 chunk 108 optimal weight: 30.0000 chunk 322 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 549 optimal weight: 40.0000 chunk 456 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 288 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 512 HIS A1049 GLN A1235 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46144 Z= 0.181 Angle : 0.635 14.927 62736 Z= 0.314 Chirality : 0.048 0.412 7340 Planarity : 0.005 0.152 8004 Dihedral : 8.644 104.798 7592 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.86 % Favored : 89.97 % Rotamer: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.76 (0.11), residues: 5672 helix: 0.99 (0.18), residues: 800 sheet: -0.30 (0.12), residues: 1928 loop : -2.51 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 433 HIS 0.004 0.000 HIS B 506 PHE 0.015 0.001 PHE B1072 TYR 0.025 0.001 TYR D1422 ARG 0.012 0.000 ARG D1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 458 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6408 (m-80) cc_final: 0.4993 (m-80) REVERT: A 430 TYR cc_start: 0.7996 (t80) cc_final: 0.7759 (t80) REVERT: A 822 PHE cc_start: 0.4920 (p90) cc_final: 0.4508 (p90) REVERT: A 954 MET cc_start: 0.4887 (tmm) cc_final: 0.4564 (tmm) REVERT: A 1245 PHE cc_start: 0.6636 (t80) cc_final: 0.6400 (t80) REVERT: A 1337 ILE cc_start: 0.7516 (mt) cc_final: 0.7189 (mt) REVERT: B 282 ILE cc_start: 0.7863 (tt) cc_final: 0.7588 (tt) REVERT: B 430 TYR cc_start: 0.8320 (t80) cc_final: 0.7860 (t80) REVERT: B 447 ARG cc_start: 0.7306 (ptm160) cc_final: 0.6993 (ptm160) REVERT: B 484 MET cc_start: 0.6962 (ppp) cc_final: 0.6049 (ppp) REVERT: C 131 TYR cc_start: 0.6118 (m-80) cc_final: 0.4935 (m-80) REVERT: C 430 TYR cc_start: 0.8011 (t80) cc_final: 0.7738 (t80) REVERT: C 451 GLU cc_start: 0.7030 (pp20) cc_final: 0.6743 (pp20) REVERT: C 822 PHE cc_start: 0.5669 (p90) cc_final: 0.4838 (p90) REVERT: C 991 VAL cc_start: 0.8736 (t) cc_final: 0.8449 (p) REVERT: C 1337 ILE cc_start: 0.7800 (mt) cc_final: 0.7566 (mt) REVERT: D 307 MET cc_start: 0.6316 (mmp) cc_final: 0.6054 (mmp) REVERT: D 430 TYR cc_start: 0.8346 (t80) cc_final: 0.7916 (t80) REVERT: D 433 TRP cc_start: 0.7187 (p-90) cc_final: 0.6930 (p-90) REVERT: D 1001 GLN cc_start: 0.6078 (tm-30) cc_final: 0.5876 (tm-30) REVERT: D 1375 ASN cc_start: 0.7217 (p0) cc_final: 0.6990 (p0) outliers start: 2 outliers final: 0 residues processed: 460 average time/residue: 0.5387 time to fit residues: 425.5575 Evaluate side-chains 339 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 529 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 313 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 310 optimal weight: 7.9990 chunk 462 optimal weight: 0.6980 chunk 306 optimal weight: 10.0000 chunk 547 optimal weight: 10.0000 chunk 342 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 252 optimal weight: 30.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A1049 GLN A1235 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1168 GLN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 46144 Z= 0.334 Angle : 0.699 21.817 62736 Z= 0.346 Chirality : 0.049 0.388 7340 Planarity : 0.006 0.178 8004 Dihedral : 8.653 103.946 7592 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.04 % Favored : 88.77 % Rotamer: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.77 (0.11), residues: 5672 helix: 0.94 (0.18), residues: 816 sheet: -0.25 (0.12), residues: 1872 loop : -2.52 (0.11), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 433 HIS 0.005 0.001 HIS A 443 PHE 0.025 0.002 PHE C 448 TYR 0.047 0.002 TYR A 268 ARG 0.011 0.001 ARG D1256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PRO cc_start: 0.6750 (OUTLIER) cc_final: 0.6473 (Cg_endo) REVERT: A 84 MET cc_start: 0.8290 (tmm) cc_final: 0.7797 (tmm) REVERT: A 131 TYR cc_start: 0.6461 (m-80) cc_final: 0.5224 (m-80) REVERT: A 430 TYR cc_start: 0.8144 (t80) cc_final: 0.7700 (t80) REVERT: A 550 ASP cc_start: 0.8303 (t0) cc_final: 0.8103 (t0) REVERT: A 822 PHE cc_start: 0.5036 (p90) cc_final: 0.4647 (p90) REVERT: A 1101 MET cc_start: 0.4389 (ptp) cc_final: 0.4009 (ptp) REVERT: A 1122 TYR cc_start: 0.5084 (t80) cc_final: 0.4857 (t80) REVERT: A 1245 PHE cc_start: 0.6645 (t80) cc_final: 0.6394 (t80) REVERT: B 430 TYR cc_start: 0.8397 (t80) cc_final: 0.7917 (t80) REVERT: B 966 MET cc_start: 0.5380 (tpp) cc_final: 0.5106 (tpp) REVERT: C 430 TYR cc_start: 0.8185 (t80) cc_final: 0.7726 (t80) REVERT: C 446 MET cc_start: 0.8323 (mmm) cc_final: 0.8074 (mmm) REVERT: C 451 GLU cc_start: 0.7332 (pp20) cc_final: 0.7000 (pp20) REVERT: C 822 PHE cc_start: 0.5684 (p90) cc_final: 0.4937 (p90) REVERT: D 430 TYR cc_start: 0.8539 (t80) cc_final: 0.8025 (t80) REVERT: D 484 MET cc_start: 0.7038 (ppp) cc_final: 0.6189 (ppp) REVERT: D 915 MET cc_start: 0.2652 (ppp) cc_final: 0.2346 (ppp) REVERT: D 1031 LYS cc_start: 0.7181 (mttm) cc_final: 0.6643 (mmtt) outliers start: 2 outliers final: 0 residues processed: 430 average time/residue: 0.5190 time to fit residues: 382.1445 Evaluate side-chains 325 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 4.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 338 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 326 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 348 optimal weight: 0.7980 chunk 372 optimal weight: 6.9990 chunk 270 optimal weight: 30.0000 chunk 51 optimal weight: 0.5980 chunk 430 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A1047 GLN A1049 GLN A1235 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 512 HIS ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 HIS ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 46144 Z= 0.197 Angle : 0.654 20.802 62736 Z= 0.321 Chirality : 0.048 0.530 7340 Planarity : 0.006 0.173 8004 Dihedral : 8.400 103.647 7592 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.05 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.02 % 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: -1.70 (0.11), residues: 5672 helix: 0.92 (0.18), residues: 816 sheet: -0.17 (0.13), residues: 1864 loop : -2.47 (0.10), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 433 HIS 0.004 0.001 HIS B 506 PHE 0.022 0.001 PHE C 83 TYR 0.024 0.001 TYR C 247 ARG 0.014 0.001 ARG D1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 4.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8281 (tmm) cc_final: 0.7789 (tmm) REVERT: A 131 TYR cc_start: 0.6133 (m-80) cc_final: 0.5295 (m-80) REVERT: A 430 TYR cc_start: 0.8085 (t80) cc_final: 0.7649 (t80) REVERT: A 822 PHE cc_start: 0.4851 (p90) cc_final: 0.4446 (p90) REVERT: A 1337 ILE cc_start: 0.7500 (mt) cc_final: 0.7147 (mt) REVERT: B 430 TYR cc_start: 0.8323 (t80) cc_final: 0.7852 (t80) REVERT: B 484 MET cc_start: 0.7343 (ppp) cc_final: 0.6499 (ppp) REVERT: C 131 TYR cc_start: 0.6378 (m-80) cc_final: 0.5016 (m-80) REVERT: C 430 TYR cc_start: 0.8100 (t80) cc_final: 0.7644 (t80) REVERT: C 446 MET cc_start: 0.8212 (mmm) cc_final: 0.7932 (mmm) REVERT: C 451 GLU cc_start: 0.6860 (pp20) cc_final: 0.6574 (pp20) REVERT: C 822 PHE cc_start: 0.5672 (p90) cc_final: 0.4900 (p90) REVERT: C 991 VAL cc_start: 0.8720 (t) cc_final: 0.8426 (p) REVERT: C 1207 MET cc_start: 0.4697 (mmt) cc_final: 0.4230 (mmt) REVERT: D 307 MET cc_start: 0.6552 (mmp) cc_final: 0.6231 (mmp) REVERT: D 430 TYR cc_start: 0.8491 (t80) cc_final: 0.7989 (t80) REVERT: D 1031 LYS cc_start: 0.7387 (mttm) cc_final: 0.6852 (mmtt) REVERT: D 1175 TYR cc_start: 0.6204 (t80) cc_final: 0.5900 (t80) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.5150 time to fit residues: 395.2423 Evaluate side-chains 335 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 498 optimal weight: 7.9990 chunk 524 optimal weight: 8.9990 chunk 478 optimal weight: 0.9980 chunk 510 optimal weight: 50.0000 chunk 307 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 400 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 461 optimal weight: 9.9990 chunk 482 optimal weight: 10.0000 chunk 508 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A1049 GLN A1235 GLN A1387 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 GLN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 251 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 210 GLN ** D 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 46144 Z= 0.418 Angle : 0.768 17.829 62736 Z= 0.382 Chirality : 0.050 0.362 7340 Planarity : 0.006 0.162 8004 Dihedral : 8.688 102.406 7592 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.88 % Favored : 87.94 % Rotamer: Outliers : 0.02 % Allowed : 1.13 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5672 helix: 0.84 (0.18), residues: 812 sheet: -0.32 (0.12), residues: 1856 loop : -2.56 (0.10), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 433 HIS 0.006 0.001 HIS A 443 PHE 0.031 0.002 PHE C 448 TYR 0.045 0.002 TYR A 268 ARG 0.011 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8339 (tmm) cc_final: 0.7902 (tmm) REVERT: A 131 TYR cc_start: 0.6630 (m-80) cc_final: 0.5521 (m-80) REVERT: A 430 TYR cc_start: 0.8240 (t80) cc_final: 0.7795 (t80) REVERT: A 822 PHE cc_start: 0.4842 (p90) cc_final: 0.4498 (p90) REVERT: B 430 TYR cc_start: 0.8465 (t80) cc_final: 0.7949 (t80) REVERT: B 1031 LYS cc_start: 0.7166 (mttm) cc_final: 0.6589 (mmtt) REVERT: C 430 TYR cc_start: 0.8305 (t80) cc_final: 0.7890 (t80) REVERT: C 446 MET cc_start: 0.8317 (mmm) cc_final: 0.8079 (mmm) REVERT: C 451 GLU cc_start: 0.7605 (pp20) cc_final: 0.7140 (pp20) REVERT: C 822 PHE cc_start: 0.5647 (p90) cc_final: 0.5001 (p90) REVERT: D 1175 TYR cc_start: 0.6183 (t80) cc_final: 0.5899 (t80) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.5359 time to fit residues: 393.8229 Evaluate side-chains 321 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 335 optimal weight: 0.8980 chunk 539 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 255 optimal weight: 30.0000 chunk 375 optimal weight: 20.0000 chunk 565 optimal weight: 20.0000 chunk 520 optimal weight: 9.9990 chunk 450 optimal weight: 0.0000 chunk 46 optimal weight: 0.8980 chunk 348 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A1049 GLN A1235 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 210 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 210 GLN D 274 ASN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46144 Z= 0.210 Angle : 0.676 15.988 62736 Z= 0.332 Chirality : 0.048 0.342 7340 Planarity : 0.006 0.154 8004 Dihedral : 8.374 102.563 7592 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.44 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.11), residues: 5672 helix: 0.93 (0.18), residues: 812 sheet: -0.26 (0.12), residues: 1880 loop : -2.47 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 433 HIS 0.006 0.001 HIS B 443 PHE 0.020 0.002 PHE D1084 TYR 0.033 0.001 TYR D 430 ARG 0.011 0.001 ARG A 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8336 (tmm) cc_final: 0.7901 (tmm) REVERT: A 131 TYR cc_start: 0.6010 (m-80) cc_final: 0.5077 (m-80) REVERT: A 430 TYR cc_start: 0.7961 (t80) cc_final: 0.7592 (t80) REVERT: A 822 PHE cc_start: 0.4712 (p90) cc_final: 0.4363 (p90) REVERT: A 915 MET cc_start: 0.2266 (ppp) cc_final: 0.1957 (ppp) REVERT: A 966 MET cc_start: 0.4478 (tpp) cc_final: 0.4234 (mmt) REVERT: A 1101 MET cc_start: 0.3696 (ptp) cc_final: 0.3376 (ptp) REVERT: A 1337 ILE cc_start: 0.7665 (mt) cc_final: 0.7294 (mt) REVERT: B 84 MET cc_start: 0.8035 (tmm) cc_final: 0.7398 (tmm) REVERT: B 430 TYR cc_start: 0.8382 (t80) cc_final: 0.7942 (t80) REVERT: B 1031 LYS cc_start: 0.7134 (mttm) cc_final: 0.6541 (mmtt) REVERT: C 84 MET cc_start: 0.8296 (tmm) cc_final: 0.7864 (tmm) REVERT: C 131 TYR cc_start: 0.6158 (m-80) cc_final: 0.5182 (m-80) REVERT: C 430 TYR cc_start: 0.8243 (t80) cc_final: 0.7770 (t80) REVERT: C 446 MET cc_start: 0.8200 (mmm) cc_final: 0.7936 (mmm) REVERT: C 451 GLU cc_start: 0.6953 (pp20) cc_final: 0.6672 (pp20) REVERT: C 822 PHE cc_start: 0.5627 (p90) cc_final: 0.5051 (p90) REVERT: C 948 LEU cc_start: 0.7250 (tt) cc_final: 0.6895 (mt) REVERT: D 377 MET cc_start: 0.8761 (mmm) cc_final: 0.7975 (mpp) REVERT: D 798 MET cc_start: 0.4592 (ptt) cc_final: 0.4207 (ptt) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.5318 time to fit residues: 400.3934 Evaluate side-chains 332 residues out of total 4976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 357 optimal weight: 0.9990 chunk 480 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 463 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1235 GLN ** A1300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.181203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.161360 restraints weight = 99313.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.159085 restraints weight = 167944.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.157442 restraints weight = 157150.602| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 46144 Z= 0.262 Angle : 0.694 15.037 62736 Z= 0.343 Chirality : 0.048 0.483 7340 Planarity : 0.006 0.151 8004 Dihedral : 8.385 102.326 7592 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.98 % Favored : 88.86 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 5672 helix: 0.88 (0.18), residues: 816 sheet: -0.25 (0.12), residues: 1864 loop : -2.47 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 433 HIS 0.005 0.001 HIS B 506 PHE 0.025 0.002 PHE C 780 TYR 0.029 0.001 TYR A 268 ARG 0.011 0.001 ARG D1000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8350.22 seconds wall clock time: 155 minutes 52.38 seconds (9352.38 seconds total)