Starting phenix.real_space_refine on Thu Feb 22 16:40:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6o_31744/02_2024/7v6o_31744.pdb" } resolution = 4.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 179 5.16 5 C 21873 2.51 5 N 5852 2.21 5 O 6912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34816 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8325 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 49, 'TRANS': 1087} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 358 Chain: "B" Number of atoms: 8446 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8440 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 280 Conformer: "B" Number of residues, atoms: 1141, 8440 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 280 bond proxies already assigned to first conformer: 8608 Chain: "C" Number of atoms: 8401 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1137, 8395 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 50, 'TRANS': 1086} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 1137, 8395 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 50, 'TRANS': 1086} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 8559 Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1574 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1615 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 3, 'ARG:plan': 1, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1602 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1644 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1600 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1609 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 4, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 26.28, per 1000 atoms: 0.75 Number of scatterers: 34816 At special positions: 0 Unit cell: (208.601, 219.58, 205.307, 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 179 16.00 O 6912 8.00 N 5852 7.00 C 21873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.02 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.70 Conformation dependent library (CDL) restraints added in 9.6 seconds 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8822 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 75 sheets defined 19.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.005A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.677A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.823A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.532A pdb=" N VAL A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.762A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'A' and resid 996 through 1011 Processing helix chain 'A' and resid 1016 through 1041 removed outlier: 3.559A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1106 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.898A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.063A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.532A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.847A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.535A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.520A pdb=" N LEU B 820 " --> pdb=" O LYS B 816 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 823 " --> pdb=" O GLN B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 940 through 958 removed outlier: 4.055A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'B' and resid 996 through 1011 Processing helix chain 'B' and resid 1016 through 1042 Processing helix chain 'B' and resid 1058 through 1106 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.615A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.765A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.173A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.573A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.994A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 809 through 813 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.603A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 940 through 958 removed outlier: 3.545A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 996 through 1011 Processing helix chain 'C' and resid 1017 through 1041 Processing helix chain 'C' and resid 1059 through 1106 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'E' and resid 203 through 208 removed outlier: 4.510A pdb=" N THR E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'G' and resid 144 through 149 removed outlier: 4.249A pdb=" N GLY G 149 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 208 removed outlier: 4.429A pdb=" N THR G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'I' and resid 144 through 149 removed outlier: 4.155A pdb=" N GLY I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 208 removed outlier: 4.521A pdb=" N THR I 207 " --> pdb=" O SER I 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 5.969A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.579A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.562A pdb=" N VAL A 263 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 283 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 265 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.409A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 367 removed outlier: 5.615A pdb=" N SER A 362 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 661 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A 364 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A 659 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.542A pdb=" N LYS A 400 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.870A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 782 Processing sheet with id=AB4, first strand: chain 'A' and resid 790 through 791 removed outlier: 4.012A pdb=" N HIS A1138 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.894A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS B 91 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 75 removed outlier: 4.219A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 86 removed outlier: 5.765A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.490A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.506A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.144A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'B' and resid 360 through 361 removed outlier: 3.515A pdb=" N VAL B 661 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 662 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 671 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 405 removed outlier: 7.083A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.040A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 605 through 607 removed outlier: 3.559A pdb=" N TYR B 606 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 613 " --> pdb=" O TYR B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 618 through 619 removed outlier: 3.523A pdb=" N GLN B 618 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 650 " --> pdb=" O GLN B 618 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 6.296A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD4, first strand: chain 'C' and resid 69 through 76 removed outlier: 5.960A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.767A pdb=" N LEU C 324 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.300A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 185 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 184 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C 239 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 186 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C 237 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU C 188 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG C 235 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.163A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 360 through 367 removed outlier: 5.729A pdb=" N SER C 362 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL C 661 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER C 364 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 659 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 671 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 400 through 405 removed outlier: 6.893A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.343A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 606 through 607 Processing sheet with id=AE4, first strand: chain 'C' and resid 778 through 783 Processing sheet with id=AE5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AE6, first strand: chain 'C' and resid 1121 through 1124 removed outlier: 7.239A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AE8, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AE9, first strand: chain 'D' and resid 13 through 16 Processing sheet with id=AF1, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.624A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 119 through 123 removed outlier: 5.621A pdb=" N LEU D 140 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER D 182 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN D 142 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 180 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AF4, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AF5, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'E' and resid 58 through 60 removed outlier: 7.263A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.651A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 194 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP E 160 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 197 " --> pdb=" O HIS E 180 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.651A pdb=" N GLY E 155 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 194 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP E 160 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR E 192 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AG1, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AG2, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AG3, first strand: chain 'F' and resid 48 through 51 removed outlier: 6.528A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.958A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.609A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AG9, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.888A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 194 " --> pdb=" O VAL G 158 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL G 197 " --> pdb=" O HIS G 180 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.888A pdb=" N GLY G 155 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 194 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 167 through 170 removed outlier: 3.713A pdb=" N HIS G 216 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR G 221 " --> pdb=" O HIS G 216 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 8 through 9 Processing sheet with id=AH4, first strand: chain 'H' and resid 13 through 16 Processing sheet with id=AH5, first strand: chain 'H' and resid 48 through 51 removed outlier: 6.520A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 88 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.558A pdb=" N ASN H 143 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=AH8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.705A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 37 through 39 removed outlier: 3.573A pdb=" N ALA I 92 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AI2, first strand: chain 'I' and resid 138 through 140 removed outlier: 3.831A pdb=" N GLY I 155 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP I 160 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR I 192 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 167 through 170 1247 hydrogen bonds defined for protein. 3312 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: 14.66 Time building geometry restraints manager: 13.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6657 1.33 - 1.45: 8769 1.45 - 1.57: 19861 1.57 - 1.69: 0 1.69 - 1.82: 226 Bond restraints: 35513 Sorted by residual: bond pdb=" N THR C1013 " pdb=" CA THR C1013 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.55e+01 bond pdb=" N THR B 741 " pdb=" CA THR B 741 " ideal model delta sigma weight residual 1.458 1.495 -0.037 7.40e-03 1.83e+04 2.52e+01 bond pdb=" N CYS A 195 " pdb=" CA CYS A 195 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.02e+01 bond pdb=" N VAL B 514 " pdb=" CA VAL B 514 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.90e+01 bond pdb=" N THR C 741 " pdb=" CA THR C 741 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.10e-03 1.21e+04 1.88e+01 ... (remaining 35508 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.58: 626 104.58 - 112.04: 16123 112.04 - 119.50: 16601 119.50 - 126.95: 14868 126.95 - 134.41: 186 Bond angle restraints: 48404 Sorted by residual: angle pdb=" C THR C 741 " pdb=" CA THR C 741 " pdb=" CB THR C 741 " ideal model delta sigma weight residual 110.71 119.26 -8.55 9.40e-01 1.13e+00 8.27e+01 angle pdb=" N ASN B 602 " pdb=" CA ASN B 602 " pdb=" C ASN B 602 " ideal model delta sigma weight residual 113.19 103.05 10.14 1.19e+00 7.06e-01 7.26e+01 angle pdb=" C ASP C 510 " pdb=" CA ASP C 510 " pdb=" CB ASP C 510 " ideal model delta sigma weight residual 109.83 117.77 -7.94 9.90e-01 1.02e+00 6.43e+01 angle pdb=" C THR B 741 " pdb=" CA THR B 741 " pdb=" CB THR B 741 " ideal model delta sigma weight residual 111.00 117.83 -6.83 8.70e-01 1.32e+00 6.17e+01 angle pdb=" CA PRO G 163 " pdb=" N PRO G 163 " pdb=" CD PRO G 163 " ideal model delta sigma weight residual 112.00 101.89 10.11 1.40e+00 5.10e-01 5.22e+01 ... (remaining 48399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 19236 16.76 - 33.52: 1427 33.52 - 50.28: 473 50.28 - 67.04: 98 67.04 - 83.80: 14 Dihedral angle restraints: 21248 sinusoidal: 7499 harmonic: 13749 Sorted by residual: dihedral pdb=" CB CYS B 679 " pdb=" SG CYS B 679 " pdb=" SG CYS B 713 " pdb=" CB CYS B 713 " ideal model delta sinusoidal sigma weight residual -86.00 -154.22 68.22 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" C GLU G 164 " pdb=" N GLU G 164 " pdb=" CA GLU G 164 " pdb=" CB GLU G 164 " ideal model delta harmonic sigma weight residual -122.60 -141.24 18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C THR C 741 " pdb=" N THR C 741 " pdb=" CA THR C 741 " pdb=" CB THR C 741 " ideal model delta harmonic sigma weight residual -122.00 -138.56 16.56 0 2.50e+00 1.60e-01 4.39e+01 ... (remaining 21245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4593 0.146 - 0.291: 1000 0.291 - 0.437: 16 0.437 - 0.582: 4 0.582 - 0.728: 2 Chirality restraints: 5615 Sorted by residual: chirality pdb=" CA PRO G 163 " pdb=" N PRO G 163 " pdb=" C PRO G 163 " pdb=" CB PRO G 163 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLU G 164 " pdb=" N GLU G 164 " pdb=" C GLU G 164 " pdb=" CB GLU G 164 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CA VAL B 604 " pdb=" N VAL B 604 " pdb=" C VAL B 604 " pdb=" CB VAL B 604 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.92e+00 ... (remaining 5612 not shown) Planarity restraints: 6304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 928 " -0.038 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C TYR C 928 " 0.132 2.00e-02 2.50e+03 pdb=" O TYR C 928 " -0.049 2.00e-02 2.50e+03 pdb=" N VAL C 929 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER B 51 " 0.034 2.00e-02 2.50e+03 7.05e-02 4.97e+01 pdb=" C BSER B 51 " -0.122 2.00e-02 2.50e+03 pdb=" O BSER B 51 " 0.046 2.00e-02 2.50e+03 pdb=" N LYS B 52 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER C 51 " -0.034 2.00e-02 2.50e+03 7.02e-02 4.93e+01 pdb=" C BSER C 51 " 0.121 2.00e-02 2.50e+03 pdb=" O BSER C 51 " -0.045 2.00e-02 2.50e+03 pdb=" N LYS C 52 " -0.042 2.00e-02 2.50e+03 ... (remaining 6301 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 15 2.35 - 2.99: 17591 2.99 - 3.62: 51785 3.62 - 4.26: 79484 4.26 - 4.90: 129428 Nonbonded interactions: 278303 Sorted by model distance: nonbonded pdb=" O LYS I 217 " pdb=" OD1 ASN I 220 " model vdw 1.712 3.040 nonbonded pdb=" OD1 ASP B 664 " pdb=" OG1 THR B 667 " model vdw 1.763 2.440 nonbonded pdb=" CG ASP B 664 " pdb=" OG1 THR B 667 " model vdw 1.908 3.270 nonbonded pdb=" O GLY B 359 " pdb=" CE2 TYR B 361 " model vdw 2.135 3.340 nonbonded pdb=" OD2 ASP B 330 " pdb=" NH2 ARG B 334 " model vdw 2.171 2.520 ... (remaining 278298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 18 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 43 or (resid 44 and (name N or na \ me CA or name C or name O or name CB )) or resid 45 through 47 or (resid 48 and \ (name N or name CA or name C or name O or name CB )) or resid 49 through 50 or r \ esid 52 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB )) or resid 58 through 61 or (resid 62 and (name N or name CA or name C or \ name O or name CB )) or resid 63 through 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 128 or (resi \ d 129 and (name N or name CA or name C or name O or name CB )) or resid 130 thro \ ugh 141 or (resid 142 and (name N or name CA or name C or name O or name CB )) o \ r resid 143 through 166 or (resid 167 through 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 200 or (resid 201 and (name N or \ name CA or name C or name O or name CB )) or resid 202 through 234 or (resid 23 \ 5 through 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 246 or (resid 247 through 249 and (name N or name CA or name C or na \ me O or name CB )) or resid 250 through 268 or (resid 269 and (name N or name CA \ or name C or name O or name CB )) or resid 270 through 279 or (resid 280 and (n \ ame N or name CA or name C or name O or name CB )) or resid 281 through 303 or ( \ resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ through 306 or (resid 307 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 340 or (resid 341 and (name \ N or name CA or name C or name O or name CB )) or resid 342 through 343 or (resi \ d 344 through 345 and (name N or name CA or name C or name O or name CB )) or re \ sid 346 through 362 or (resid 363 and (name N or name CA or name C or name O or \ name CB )) or resid 364 through 365 or (resid 366 and (name N or name CA or name \ C or name O or name CB )) or resid 367 through 368 or (resid 369 and (name N or \ name CA or name C or name O or name CB )) or resid 370 through 373 or (resid 37 \ 4 through 375 and (name N or name CA or name C or name O or name CB )) or resid \ 376 through 377 or resid 382 through 387 or (resid 388 and (name N or name CA or \ name C or name O or name CB )) or resid 389 through 396 or (resid 397 and (name \ N or name CA or name C or name O or name CB )) or resid 398 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 408 or (resid 409 through 410 and (name N or name CA or name C or name O or \ name CB )) or resid 411 through 463 or (resid 464 through 466 and (name N or na \ me CA or name C or name O or name CB )) or resid 467 or (resid 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 482 or (resid 4 \ 83 through 484 and (name N or name CA or name C or name O or name CB )) or resid \ 485 through 496 or (resid 497 and (name N or name CA or name C or name O or nam \ e CB )) or resid 498 through 539 or (resid 540 and (name N or name CA or name C \ or name O or name CB )) or resid 541 or (resid 542 through 543 and (name N or na \ me CA or name C or name O or name CB )) or resid 544 through 558 or (resid 559 a \ nd (name N or name CA or name C or name O or name CB )) or resid 560 through 562 \ or (resid 563 through 567 and (name N or name CA or name C or name O or name CB \ )) or resid 568 through 581 or (resid 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 or (resid 584 and (name N or name CA or name C \ or name O or name CB )) or resid 585 through 586 or (resid 595 and (name N or na \ me CA or name C or name O or name CB )) or resid 597 through 598 or (resid 599 t \ hrough 600 and (name N or name CA or name C or name O or name CB )) or resid 601 \ through 643 or (resid 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 646 or (resid 647 and (name N or name CA or name C or n \ ame O or name CB )) or resid 648 through 656 or (resid 657 and (name N or name C \ A or name C or name O or name CB )) or resid 658 through 659 or (resid 660 and ( \ name N or name CA or name C or name O or name CB )) or resid 661 through 662 or \ (resid 663 through 666 and (name N or name CA or name C or name O or name CB )) \ or resid 667 through 690 or (resid 691 and (name N or name CA or name C or name \ O or name CB )) or resid 692 through 693 or (resid 694 and (name N or name CA or \ name C or name O or name CB )) or resid 695 through 714 or (resid 715 and (name \ N or name CA or name C or name O or name CB )) or resid 716 through 739 or (res \ id 740 and (name N or name CA or name C or name O or name CB )) or resid 741 thr \ ough 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) \ or resid 781 through 784 or (resid 785 through 786 and (name N or name CA or nam \ e C or name O or name CB )) or resid 787 through 798 or (resid 799 and (name N o \ r name CA or name C or name O or name CB )) or resid 800 through 808 or (resid 8 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 810 through \ 841 or (resid 842 and (name N or name CA or name C or name O or name CB )) or r \ esid 843 through 844 or (resid 845 and (name N or name CA or name C or name O or \ name CB )) or resid 846 through 848 or (resid 849 and (name N or name CA or nam \ e C or name O or name CB )) or resid 850 through 851 or (resid 852 and (name N o \ r name CA or name C or name O or name CB )) or resid 853 or (resid 854 and (name \ N or name CA or name C or name O or name CB )) or resid 855 or (resid 856 and ( \ name N or name CA or name C or name O or name CB )) or resid 857 through 868 or \ (resid 869 through 871 and (name N or name CA or name C or name O or name CB )) \ or resid 872 or (resid 873 and (name N or name CA or name C or name O or name CB \ )) or resid 874 through 886 or (resid 887 and (name N or name CA or name C or n \ ame O or name CB )) or resid 888 through 889 or (resid 890 and (name N or name C \ A or name C or name O or name CB )) or resid 891 through 892 or (resid 893 and ( \ name N or name CA or name C or name O or name CB )) or resid 894 through 896 or \ (resid 897 and (name N or name CA or name C or name O or name CB )) or resid 898 \ through 908 or (resid 909 and (name N or name CA or name C or name O or name CB \ )) or resid 910 through 912 or (resid 913 through 914 and (name N or name CA or \ name C or name O or name CB )) or resid 915 through 938 or (resid 939 and (name \ N or name CA or name C or name O or name CB )) or resid 940 through 949 or (res \ id 950 and (name N or name CA or name C or name O or name CB )) or resid 951 thr \ ough 959 or (resid 960 and (name N or name CA or name C or name O or name CB )) \ or resid 961 through 963 or (resid 964 and (name N or name CA or name C or name \ O or name CB )) or resid 965 through 973 or (resid 974 and (name N or name CA or \ name C or name O or name CB )) or resid 975 through 984 or (resid 985 through 9 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 988 through \ 989 or (resid 990 and (name N or name CA or name C or name O or name CB )) or r \ esid 991 through 992 or (resid 993 and (name N or name CA or name C or name O or \ name CB )) or resid 994 through 1008 or (resid 1009 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1010 through 1016 or (resid 1017 through \ 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 or ( \ resid 1020 and (name N or name CA or name C or name O or name CB )) or resid 102 \ 1 through 1030 or (resid 1031 through 1032 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1033 through 1034 or (resid 1035 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1036 through 1039 or (resid 1040 \ and (name N or name CA or name C or name O or name CB )) or resid 1041 through \ 1053 or (resid 1054 and (name N or name CA or name C or name O or name CB )) or \ resid 1055 through 1073 or (resid 1074 and (name N or name CA or name C or name \ O or name CB )) or resid 1075 through 1076 or (resid 1077 and (name N or name CA \ or name C or name O or name CB )) or resid 1078 through 1083 or (resid 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1087 \ or (resid 1088 and (name N or name CA or name C or name O or name CB )) or resi \ d 1089 through 1096 or (resid 1097 and (name N or name CA or name C or name O or \ name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or name CA or \ name C or name O or name CB )) or resid 1101 or (resid 1102 and (name N or name \ CA or name C or name O or name CB )) or resid 1103 through 1109 or resid 1111 th \ rough 1112 or (resid 1113 and (name N or name CA or name C or name O or name CB \ )) or resid 1114 through 1115 or (resid 1116 and (name N or name CA or name C or \ name O or name CB )) or resid 1117 through 1121 or (resid 1122 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1123 through 1124 or (resid 11 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 1126 throug \ h 1135 or (resid 1136 through 1139 and (name N or name CA or name C or name O or \ name CB )) or resid 1140 through 1150 or (resid 1151 through 1153 and (name N o \ r name CA or name C or name O or name CB )) or resid 1154 through 1176 or (resid \ 1177 and (name N or name CA or name C or name O or name CB )) or resid 1178 or \ (resid 1179 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 80 through 1181 or (resid 1182 through 1184 and (name N or name CA or name C or \ name O or name CB )) or resid 1185 through 1191 or (resid 1192 through 1193 and \ (name N or name CA or name C or name O or name CB )) or resid 1194 through 1206) \ ) selection = (chain 'B' and (resid 18 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 43 or (resid 44 and (name N or nam \ e CA or name C or name O or name CB )) or resid 45 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 50 or re \ sid 52 through 63 or (resid 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA \ or name C or name O or name CB )) or resid 81 through 96 or (resid 98 through 10 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 102 through \ 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or re \ sid 106 through 111 or (resid 112 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 114 through 125 or (resid 126 and (name N or nam \ e CA or name C or name O or name CB )) or resid 127 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 139 \ or (resid 140 and (name N or name CA or name C or name O or name CB )) or resid \ 141 through 143 or (resid 144 and (name N or name CA or name C or name O or name \ CB )) or resid 145 through 147 or (resid 148 through 149 and (name N or name CA \ or name C or name O or name CB )) or resid 150 through 163 or (resid 164 and (n \ ame N or name CA or name C or name O or name CB )) or resid 165 through 180 or ( \ resid 181 through 184 and (name N or name CA or name C or name O or name CB )) o \ r resid 185 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 or (resid 190 and (name N or name CA or name C or na \ me O or name CB )) or resid 191 through 198 or (resid 199 and (name N or name CA \ or name C or name O or name CB )) or resid 200 through 203 or (resid 204 throug \ h 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thro \ ugh 221 or (resid 222 through 223 and (name N or name CA or name C or name O or \ name CB )) or resid 224 through 228 or (resid 229 and (name N or name CA or name \ C or name O or name CB )) or resid 230 through 233 or (resid 234 through 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 through 244 \ or (resid 245 and (name N or name CA or name C or name O or name CB )) or resid \ 246 through 248 or (resid 249 and (name N or name CA or name C or name O or name \ CB )) or resid 250 through 257 or (resid 258 and (name N or name CA or name C o \ r name O or name CB )) or resid 259 through 262 or (resid 263 and (name N or nam \ e CA or name C or name O or name CB )) or resid 264 through 279 or (resid 280 an \ d (name N or name CA or name C or name O or name CB )) or resid 281 through 283 \ or (resid 284 and (name N or name CA or name C or name O or name CB )) or resid \ 285 through 288 or (resid 289 through 291 and (name N or name CA or name C or na \ me O or name CB )) or resid 292 through 300 or (resid 301 and (name N or name CA \ or name C or name O or name CB )) or resid 302 through 307 or (resid 308 throug \ h 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 312 or (resid 313 through 314 and (name N or name CA or name C or name O or \ name CB )) or resid 315 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 325 or (resid 326 and (name N or \ name CA or name C or name O or name CB )) or resid 327 through 340 or (resid 34 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 342 or (resi \ d 343 through 345 and (name N or name CA or name C or name O or name CB )) or re \ sid 346 through 353 or (resid 354 and (name N or name CA or name C or name O or \ name CB )) or resid 355 through 373 or (resid 374 through 375 and (name N or nam \ e CA or name C or name O or name CB )) or resid 376 through 377 or (resid 382 an \ d (name N or name CA or name C or name O or name CB )) or resid 383 through 400 \ or (resid 401 and (name N or name CA or name C or name O or name CB )) or resid \ 402 through 405 or (resid 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 or (resid 408 through 410 and (name N or name CA or name C o \ r name O or name CB )) or resid 411 through 437 or (resid 438 and (name N or nam \ e CA or name C or name O or name CB )) or resid 439 through 441 or (resid 442 an \ d (name N or name CA or name C or name O or name CB )) or resid 443 or (resid 44 \ 4 through 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 464 or (resid 465 through 466 and (name N or name CA or name C or na \ me O or name CB )) or resid 467 through 470 or (resid 471 and (name N or name CA \ or name C or name O or name CB )) or resid 472 through 474 or (resid 475 and (n \ ame N or name CA or name C or name O or name CB )) or resid 476 through 482 or ( \ resid 483 through 484 and (name N or name CA or name C or name O or name CB )) o \ r resid 485 through 490 or (resid 491 and (name N or name CA or name C or name O \ or name CB )) or resid 492 through 504 or (resid 505 and (name N or name CA or \ name C or name O or name CB )) or resid 506 through 520 or (resid 521 and (name \ N or name CA or name C or name O or name CB )) or resid 522 through 523 or (resi \ d 524 and (name N or name CA or name C or name O or name CB )) or resid 525 or ( \ resid 526 through 527 and (name N or name CA or name C or name O or name CB )) o \ r resid 528 through 558 or (resid 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 565 or (resid 566 through 567 and (name N or \ name CA or name C or name O or name CB )) or resid 568 or (resid 569 and (name \ N or name CA or name C or name O or name CB )) or resid 570 or (resid 571 and (n \ ame N or name CA or name C or name O or name CB )) or resid 572 through 575 or ( \ resid 576 through 577 and (name N or name CA or name C or name O or name CB )) o \ r resid 578 through 581 or (resid 582 and (name N or name CA or name C or name O \ or name CB )) or resid 583 through 586 or (resid 587 and (name N or name CA or \ name C or name O or name CB )) or resid 597 through 598 or (resid 599 through 60 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 601 through \ 606 or (resid 607 and (name N or name CA or name C or name O or name CB )) or re \ sid 608 through 631 or (resid 632 and (name N or name CA or name C or name O or \ name CB )) or resid 633 through 635 or (resid 636 and (name N or name CA or name \ C or name O or name CB )) or resid 637 through 659 or (resid 660 and (name N or \ name CA or name C or name O or name CB )) or resid 661 through 662 or (resid 66 \ 3 through 666 and (name N or name CA or name C or name O or name CB )) or resid \ 667 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 690 or (resid 691 and (name N or name CA or name C o \ r name O or name CB )) or resid 692 through 693 or (resid 694 and (name N or nam \ e CA or name C or name O or name CB )) or resid 695 through 776 or resid 778 thr \ ough 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) \ or resid 781 through 784 or (resid 785 through 786 and (name N or name CA or nam \ e C or name O or name CB )) or resid 787 through 792 or (resid 793 and (name N o \ r name CA or name C or name O or name CB )) or resid 794 through 806 or (resid 8 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 808 through \ 840 or (resid 841 through 842 and (name N or name CA or name C or name O or nam \ e CB )) or resid 843 through 853 or (resid 854 and (name N or name CA or name C \ or name O or name CB )) or resid 855 or (resid 856 and (name N or name CA or nam \ e C or name O or name CB )) or resid 857 through 868 or (resid 869 through 871 a \ nd (name N or name CA or name C or name O or name CB )) or resid 872 through 924 \ or (resid 925 through 926 and (name N or name CA or name C or name O or name CB \ )) or resid 927 through 938 or (resid 939 and (name N or name CA or name C or n \ ame O or name CB )) or resid 940 through 949 or (resid 950 and (name N or name C \ A or name C or name O or name CB )) or resid 951 through 959 or (resid 960 and ( \ name N or name CA or name C or name O or name CB )) or resid 961 through 966 or \ (resid 967 through 969 and (name N or name CA or name C or name O or name CB )) \ or resid 970 through 973 or (resid 974 and (name N or name CA or name C or name \ O or name CB )) or resid 975 through 976 or (resid 977 and (name N or name CA or \ name C or name O or name CB )) or resid 978 through 984 or (resid 985 through 9 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 988 through \ 989 or (resid 990 and (name N or name CA or name C or name O or name CB )) or r \ esid 991 through 992 or (resid 993 and (name N or name CA or name C or name O or \ name CB )) or resid 994 through 1011 or (resid 1012 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1013 through 1015 or (resid 1016 through \ 1018 and (name N or name CA or name C or name O or name CB )) or resid 1019 thro \ ugh 1039 or (resid 1040 and (name N or name CA or name C or name O or name CB )) \ or resid 1041 through 1052 or (resid 1053 through 1054 and (name N or name CA o \ r name C or name O or name CB )) or resid 1055 through 1056 or (resid 1057 and ( \ name N or name CA or name C or name O or name CB )) or resid 1058 through 1061 o \ r (resid 1062 through 1063 and (name N or name CA or name C or name O or name CB \ )) or resid 1064 through 1065 or (resid 1066 and (name N or name CA or name C o \ r name O or name CB )) or resid 1067 or (resid 1068 through 1069 and (name N or \ name CA or name C or name O or name CB )) or resid 1070 through 1096 or (resid 1 \ 097 and (name N or name CA or name C or name O or name CB )) or resid 1098 throu \ gh 1099 or (resid 1100 and (name N or name CA or name C or name O or name CB )) \ or resid 1101 or (resid 1102 and (name N or name CA or name C or name O or name \ CB )) or resid 1103 through 1104 or (resid 1105 and (name N or name CA or name C \ or name O or name CB )) or resid 1106 through 1109 or resid 1111 or (resid 1112 \ through 1113 and (name N or name CA or name C or name O or name CB )) or resid \ 1114 through 1124 or (resid 1125 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1126 through 1150 or (resid 1151 through 1153 and (name N or \ name CA or name C or name O or name CB )) or resid 1154 or (resid 1155 through 1 \ 156 and (name N or name CA or name C or name O or name CB )) or resid 1157 throu \ gh 1170 or (resid 1171 through 1172 and (name N or name CA or name C or name O o \ r name CB )) or resid 1173 through 1181 or (resid 1182 through 1184 and (name N \ or name CA or name C or name O or name CB )) or resid 1185 or (resid 1186 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1187 through 1191 or \ (resid 1192 through 1193 and (name N or name CA or name C or name O or name CB \ )) or resid 1194 through 1197 or (resid 1198 and (name N or name CA or name C or \ name O or name CB )) or resid 1199 through 1206)) selection = (chain 'C' and ((resid 18 through 19 and (name N or name CA or name C or name O \ or name CB )) or resid 20 through 50 or resid 52 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 90 or (resid 91 through 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 through 96 or (resid 98 through 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 111 or (r \ esid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 125 or (resid 126 and (name N or name CA or name C or name O \ or name CB )) or resid 127 through 139 or (resid 140 and (name N or name CA or n \ ame C or name O or name CB )) or resid 141 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 145 through 148 or (resid \ 149 and (name N or name CA or name C or name O or name CB )) or resid 150 throu \ gh 166 or (resid 167 through 168 and (name N or name CA or name C or name O or n \ ame CB )) or resid 169 through 179 or (resid 180 through 184 and (name N or name \ CA or name C or name O or name CB )) or resid 185 through 187 or (resid 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 or (resid 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 2 \ 19 or (resid 220 through 223 and (name N or name CA or name C or name O or name \ CB )) or resid 224 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 through 235 or (resid 236 and (name N or name \ CA or name C or name O or name CB )) or resid 237 through 244 or (resid 245 and \ (name N or name CA or name C or name O or name CB )) or resid 246 or (resid 247 \ through 249 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 50 through 262 or (resid 263 and (name N or name CA or name C or name O or name \ CB )) or resid 264 through 283 or (resid 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 288 or (resid 289 through 291 and (na \ me N or name CA or name C or name O or name CB )) or resid 292 through 300 or (r \ esid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 t \ hrough 303 or (resid 304 and (name N or name CA or name C or name O or name CB ) \ ) or resid 305 through 306 or (resid 307 through 309 and (name N or name CA or n \ ame C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 through 325 or (resid 326 and (name N or name CA or name C or name O or n \ ame CB )) or resid 327 through 342 or (resid 343 through 345 and (name N or name \ CA or name C or name O or name CB )) or resid 346 through 353 or (resid 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 362 o \ r (resid 363 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 64 through 368 or (resid 369 and (name N or name CA or name C or name O or name \ CB )) or resid 370 through 374 or (resid 375 and (name N or name CA or name C or \ name O or name CB )) or resid 376 through 387 or (resid 388 and (name N or name \ CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 and \ (name N or name CA or name C or name O or name CB )) or resid 398 through 399 o \ r (resid 400 through 401 and (name N or name CA or name C or name O or name CB ) \ ) or resid 402 through 441 or (resid 442 and (name N or name CA or name C or nam \ e O or name CB )) or resid 443 or (resid 444 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 through 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 467 or (r \ esid 468 and (name N or name CA or name C or name O or name CB )) or resid 469 t \ hrough 470 or (resid 471 and (name N or name CA or name C or name O or name CB ) \ ) or resid 472 through 474 or (resid 475 and (name N or name CA or name C or nam \ e O or name CB )) or resid 476 through 492 or (resid 493 and (name N or name CA \ or name C or name O or name CB )) or resid 494 through 496 or (resid 497 and (na \ me N or name CA or name C or name O or name CB )) or resid 498 through 504 or (r \ esid 505 and (name N or name CA or name C or name O or name CB )) or resid 506 t \ hrough 522 or (resid 523 through 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 or (resid 526 through 527 and (name N or name CA or n \ ame C or name O or name CB )) or resid 528 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or resid 541 or (resid 542 through \ 543 and (name N or name CA or name C or name O or name CB )) or resid 544 throu \ gh 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) or \ resid 554 through 562 or (resid 563 through 567 and (name N or name CA or name \ C or name O or name CB )) or resid 568 or (resid 569 and (name N or name CA or n \ ame C or name O or name CB )) or resid 570 or (resid 571 and (name N or name CA \ or name C or name O or name CB )) or resid 572 through 575 or (resid 576 through \ 577 and (name N or name CA or name C or name O or name CB )) or resid 578 throu \ gh 587 or resid 597 through 604 or (resid 605 through 607 and (name N or name CA \ or name C or name O or name CB )) or resid 608 through 631 or (resid 632 and (n \ ame N or name CA or name C or name O or name CB )) or resid 633 through 635 or ( \ resid 636 and (name N or name CA or name C or name O or name CB )) or resid 637 \ through 643 or (resid 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 646 or (resid 647 and (name N or name CA or name C or na \ me O or name CB )) or resid 648 through 656 or (resid 657 and (name N or name CA \ or name C or name O or name CB )) or resid 658 through 685 or (resid 686 and (n \ ame N or name CA or name C or name O or name CB )) or resid 687 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 739 or (resid 740 and (name N or name CA or name C or name O or name CB \ )) or resid 741 through 776 or resid 778 through 785 or (resid 786 and (name N o \ r name CA or name C or name O or name CB )) or resid 787 through 798 or (resid 7 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 800 through \ 806 or (resid 807 and (name N or name CA or name C or name O or name CB )) or r \ esid 808 or (resid 809 and (name N or name CA or name C or name O or name CB )) \ or resid 810 through 840 or (resid 841 through 842 and (name N or name CA or nam \ e C or name O or name CB )) or resid 843 through 844 or (resid 845 and (name N o \ r name CA or name C or name O or name CB )) or resid 846 through 848 or (resid 8 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 850 through \ 851 or (resid 852 and (name N or name CA or name C or name O or name CB )) or r \ esid 853 through 872 or (resid 873 and (name N or name CA or name C or name O or \ name CB )) or resid 874 through 886 or (resid 887 and (name N or name CA or nam \ e C or name O or name CB )) or resid 888 through 889 or (resid 890 and (name N o \ r name CA or name C or name O or name CB )) or resid 891 through 892 or (resid 8 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 894 through \ 896 or (resid 897 and (name N or name CA or name C or name O or name CB )) or r \ esid 898 through 908 or (resid 909 and (name N or name CA or name C or name O or \ name CB )) or resid 910 through 912 or (resid 913 through 914 and (name N or na \ me CA or name C or name O or name CB )) or resid 915 through 924 or (resid 925 t \ hrough 926 and (name N or name CA or name C or name O or name CB )) or resid 927 \ through 963 or (resid 964 and (name N or name CA or name C or name O or name CB \ )) or resid 965 through 976 or (resid 977 and (name N or name CA or name C or n \ ame O or name CB )) or resid 978 through 986 or (resid 987 and (name N or name C \ A or name C or name O or name CB )) or resid 988 through 1008 or (resid 1009 and \ (name N or name CA or name C or name O or name CB )) or resid 1010 through 1011 \ or (resid 1012 and (name N or name CA or name C or name O or name CB )) or resi \ d 1013 through 1015 or (resid 1016 through 1018 and (name N or name CA or name C \ or name O or name CB )) or resid 1019 or (resid 1020 and (name N or name CA or \ name C or name O or name CB )) or resid 1021 through 1030 or (resid 1031 through \ 1032 and (name N or name CA or name C or name O or name CB )) or resid 1033 thr \ ough 1034 or (resid 1035 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1036 through 1052 or (resid 1053 through 1054 and (name N or name CA \ or name C or name O or name CB )) or resid 1055 through 1056 or (resid 1057 and \ (name N or name CA or name C or name O or name CB )) or resid 1058 through 1061 \ or (resid 1062 through 1063 and (name N or name CA or name C or name O or name C \ B )) or resid 1064 through 1065 or (resid 1066 and (name N or name CA or name C \ or name O or name CB )) or resid 1067 or (resid 1068 through 1069 and (name N or \ name CA or name C or name O or name CB )) or resid 1070 through 1083 or (resid \ 1084 and (name N or name CA or name C or name O or name CB )) or resid 1085 thro \ ugh 1087 or (resid 1088 and (name N or name CA or name C or name O or name CB )) \ or resid 1089 through 1104 or (resid 1105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1106 through 1111 or (resid 1112 through 1113 and ( \ name N or name CA or name C or name O or name CB )) or resid 1114 through 1135 o \ r (resid 1136 through 1139 and (name N or name CA or name C or name O or name CB \ )) or resid 1140 through 1154 or (resid 1155 through 1156 and (name N or name C \ A or name C or name O or name CB )) or resid 1157 through 1197 or (resid 1198 an \ d (name N or name CA or name C or name O or name CB )) or resid 1199 through 120 \ 6)) } ncs_group { reference = (chain 'D' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 13 or (resid 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 88 or (resid 89 and (nam \ e N or name CA or name C or name O or name CB )) or resid 90 through 98 or (resi \ d 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throu \ gh 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 136 or (resid 137 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 140 or (resid 141 and (name N or \ name CA or name C or name O or name CB )) or resid 142 through 150 or (resid 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 1 \ 68 or (resid 169 and (name N or name CA or name C or name O or name CB )) or res \ id 170 through 177 or (resid 178 through 179 and (name N or name CA or name C or \ name O or name CB )) or resid 180 through 186 or (resid 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 200 o \ r (resid 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213 or (resid 214 and (name N or name CA or name C or name O or name \ CB )) or resid 215 through 219)) selection = (chain 'F' and (resid 4 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 13 or (resid 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 19 or (resid 20 through \ 21 and (name N or name CA or name C or name O or name CB )) or resid 22 through \ 36 or (resid 37 through 40 and (name N or name CA or name C or name O or name CB \ )) or resid 41 through 80 or (resid 81 and (name N or name CA or name C or name \ O or name CB )) or resid 82 through 85 or (resid 86 through 87 and (name N or n \ ame CA or name C or name O or name CB )) or resid 88 or (resid 89 and (name N or \ name CA or name C or name O or name CB )) or resid 90 through 100 or (resid 101 \ and (name N or name CA or name C or name O or name CB )) or resid 102 through 1 \ 06 or (resid 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 112 or (resid 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 175 or (resid 176 through 179 and \ (name N or name CA or name C or name O or name CB )) or resid 180 through 190 o \ r (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 92 through 219)) selection = (chain 'H' and (resid 4 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 36 or (resid 37 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 85 or (resid 86 through 87 and (name N or name CA or name C or name \ O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA or n \ ame C or name O or name CB )) or resid 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 136 or (r \ esid 137 through 138 and (name N or name CA or name C or name O or name CB )) or \ resid 139 through 150 or (resid 151 and (name N or name CA or name C or name O \ or name CB )) or resid 152 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 175 or (resid 176 through 179 \ and (name N or name CA or name C or name O or name CB )) or resid 180 through 2 \ 13 or (resid 214 and (name N or name CA or name C or name O or name CB )) or res \ id 215 through 219)) } ncs_group { reference = (chain 'E' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 45 or (resid 46 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 61 or resid \ 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or res \ id 65 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 78 or (resid 79 and (name N or name CA or name C or n \ ame O or name CB )) or resid 80 or (resid 81 and (name N or name CA or name C or \ name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 102 or (resid 103 throu \ gh 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thr \ ough 109 or (resid 110 through 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 117 through 227)) selection = (chain 'G' and (resid 3 or (resid 4 and (name N or name CA or name C or name O o \ r name CB )) or resid 5 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 45 or (resid 46 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 56 or (resi \ d 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throug \ h 59 or (resid 60 through 61 and (name N or name CA or name C or name O or name \ CB )) or resid 63 through 66 or (resid 67 through 68 and (name N or name CA or n \ ame C or name O or name CB )) or resid 69 through 82 or (resid 83 and (name N or \ name CA or name C or name O or name CB )) or resid 84 through 101 or (resid 102 \ through 105 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 06 through 110 or (resid 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 through 139 or (resid 140 through 141 and (name N or name CA \ or name C or name O or name CB )) or resid 142 through 227)) selection = (chain 'I' and (resid 3 through 19 or resid 21 through 49 or (resid 50 through 5 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 53 through 5 \ 6 or (resid 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 through 59 or (resid 60 through 61 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or nam \ e O or name CB )) or resid 65 through 78 or (resid 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 102 or (resid 10 \ 3 through 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 109 or (resid 110 through 111 and (name N or name CA or name C or na \ me O or name CB )) or resid 112 through 115 or (resid 116 and (name N or name CA \ or name C or name O or name CB )) or resid 117 through 136 or (resid 137 and (n \ ame N or name CA or name C or name O or name CB )) or resid 138 through 139 or ( \ resid 140 through 141 and (name N or name CA or name C or name O or name CB )) o \ r resid 142 through 227)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 1.350 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: 0.040 Extract box with map and model: 8.700 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 101.600 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.220 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.013 0.049 35513 Z= 0.885 Angle : 1.540 13.559 48404 Z= 1.188 Chirality : 0.107 0.728 5615 Planarity : 0.004 0.083 6304 Dihedral : 13.449 83.799 12285 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.04 % Favored : 95.06 % Rotamer: Outliers : 7.18 % Allowed : 9.71 % Favored : 83.10 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.12), residues: 4679 helix: 4.15 (0.17), residues: 776 sheet: 1.88 (0.15), residues: 1196 loop : -0.42 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 120 HIS 0.020 0.001 HIS I 35 PHE 0.016 0.002 PHE C 156 TYR 0.031 0.002 TYR B 794 ARG 0.005 0.001 ARG B1057 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 374 time to evaluate : 3.658 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: 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 404 PHE cc_start: 0.6805 (m-80) cc_final: 0.6524 (m-80) REVERT: A 784 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.5282 (m) REVERT: A 794 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 985 ILE cc_start: 0.5467 (OUTLIER) cc_final: 0.4837 (tt) REVERT: A 1036 LEU cc_start: 0.8315 (mt) cc_final: 0.7858 (mt) REVERT: A 1042 ASN cc_start: 0.7748 (m110) cc_final: 0.7538 (t0) REVERT: A 1117 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7362 (p) REVERT: A 1180 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.6053 (mp) REVERT: B 32 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5680 (pm20) REVERT: B 232 PHE cc_start: 0.6892 (m-80) cc_final: 0.6214 (m-80) REVERT: B 324 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6853 (tp) REVERT: B 694 ARG cc_start: 0.6792 (tpm170) cc_final: 0.6296 (tmt170) REVERT: B 759 LEU cc_start: 0.5021 (OUTLIER) cc_final: 0.4804 (mp) REVERT: B 1005 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8919 (mp) REVERT: B 1047 ILE cc_start: 0.6685 (tt) cc_final: 0.6429 (tt) REVERT: B 1123 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8420 (mm) REVERT: C 290 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8194 (mm) REVERT: C 363 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6786 (t) REVERT: C 786 PHE cc_start: 0.7786 (m-80) cc_final: 0.7463 (m-80) REVERT: C 817 CYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6499 (p) REVERT: C 894 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8861 (pp) REVERT: C 932 TYR cc_start: 0.5086 (p90) cc_final: 0.4881 (p90) REVERT: C 1047 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5100 (tp) REVERT: C 1187 THR cc_start: 0.6227 (OUTLIER) cc_final: 0.6001 (p) REVERT: D 22 VAL cc_start: 0.6238 (OUTLIER) cc_final: 0.6025 (t) REVERT: D 24 ILE cc_start: 0.4280 (OUTLIER) cc_final: 0.3874 (mt) REVERT: D 103 PHE cc_start: 0.7986 (p90) cc_final: 0.7703 (p90) REVERT: D 128 GLU cc_start: 0.3088 (OUTLIER) cc_final: 0.2703 (pp20) REVERT: D 173 SER cc_start: 0.4604 (m) cc_final: 0.4357 (t) REVERT: E 34 MET cc_start: 0.8196 (tpp) cc_final: 0.7565 (ttt) REVERT: E 100 ASN cc_start: 0.4737 (m110) cc_final: 0.3591 (m110) REVERT: F 5 ILE cc_start: 0.5169 (OUTLIER) cc_final: 0.4690 (tp) REVERT: F 18 VAL cc_start: 0.8137 (t) cc_final: 0.7889 (t) REVERT: G 35 HIS cc_start: 0.8533 (m-70) cc_final: 0.8031 (m90) REVERT: H 7 MET cc_start: 0.4852 (tmm) cc_final: 0.3256 (mpp) REVERT: H 128 GLU cc_start: -0.1984 (OUTLIER) cc_final: -0.2581 (pt0) REVERT: I 35 HIS cc_start: 0.3560 (OUTLIER) cc_final: 0.2066 (m-70) REVERT: I 118 ASP cc_start: 0.6207 (t0) cc_final: 0.5958 (t0) REVERT: I 211 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6963 (tt) outliers start: 264 outliers final: 49 residues processed: 602 average time/residue: 0.4424 time to fit residues: 436.9828 Evaluate side-chains 249 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 177 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 396 optimal weight: 40.0000 chunk 355 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 367 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 425 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 398 ASN A 765 ASN A 785 ASN A 839 ASN A 993 ASN A 999 ASN A1079 ASN A1085 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** A1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 277 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN B 627 GLN B 857 GLN B 981 ASN B 999 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 111 GLN C 114 ASN C 226 ASN C 681 HIS ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 ASN ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN F 37 ASN F 157 ASN G 82 GLN G 187 GLN H 37 ASN H 40 GLN H 93 GLN H 157 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 35513 Z= 0.305 Angle : 0.753 10.504 48404 Z= 0.400 Chirality : 0.049 0.311 5615 Planarity : 0.006 0.136 6304 Dihedral : 5.300 46.945 5052 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.30 % Favored : 96.38 % Rotamer: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 4679 helix: 2.01 (0.18), residues: 791 sheet: 1.38 (0.15), residues: 1206 loop : -0.75 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 253 HIS 0.016 0.002 HIS I 35 PHE 0.026 0.002 PHE G 27 TYR 0.043 0.003 TYR H 145 ARG 0.008 0.001 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7021 (tpp) cc_final: 0.6746 (mmm) REVERT: A 641 TYR cc_start: 0.4437 (p90) cc_final: 0.3901 (p90) REVERT: A 798 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 913 MET cc_start: 0.7082 (mpp) cc_final: 0.6669 (mpp) REVERT: B 84 MET cc_start: 0.9037 (tmm) cc_final: 0.8717 (tmm) REVERT: B 939 MET cc_start: 0.8361 (tpt) cc_final: 0.7860 (tpp) REVERT: C 147 PHE cc_start: 0.8447 (m-80) cc_final: 0.8080 (m-80) REVERT: C 786 PHE cc_start: 0.7520 (m-80) cc_final: 0.7316 (m-80) REVERT: E 34 MET cc_start: 0.8200 (tpp) cc_final: 0.7903 (ttm) REVERT: E 83 MET cc_start: 0.6656 (mpp) cc_final: 0.5380 (tpp) REVERT: E 86 LEU cc_start: 0.6329 (tt) cc_final: 0.5403 (pp) REVERT: G 163 PRO cc_start: 0.6030 (OUTLIER) cc_final: 0.5744 (Cg_endo) REVERT: H 111 ILE cc_start: 0.6964 (mp) cc_final: 0.6316 (mm) REVERT: I 74 ASN cc_start: 0.8760 (m-40) cc_final: 0.8548 (t0) outliers start: 5 outliers final: 0 residues processed: 204 average time/residue: 0.4856 time to fit residues: 162.0497 Evaluate side-chains 130 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 236 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 354 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 426 optimal weight: 0.8980 chunk 460 optimal weight: 7.9990 chunk 379 optimal weight: 50.0000 chunk 423 optimal weight: 30.0000 chunk 145 optimal weight: 0.3980 chunk 342 optimal weight: 40.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 627 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN A1201 ASN B 319 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 475 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN F 40 GLN G 35 HIS ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35513 Z= 0.167 Angle : 0.597 9.290 48404 Z= 0.316 Chirality : 0.044 0.276 5615 Planarity : 0.004 0.128 6304 Dihedral : 4.754 46.912 5052 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.24 % Favored : 95.44 % Rotamer: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.12), residues: 4679 helix: 2.18 (0.18), residues: 789 sheet: 1.13 (0.14), residues: 1229 loop : -0.84 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 38 HIS 0.015 0.001 HIS C 766 PHE 0.024 0.001 PHE C 228 TYR 0.031 0.001 TYR B 794 ARG 0.011 0.001 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.6962 (tpp) cc_final: 0.6667 (mmm) REVERT: A 641 TYR cc_start: 0.4197 (p90) cc_final: 0.3903 (p90) REVERT: A 913 MET cc_start: 0.6992 (mpp) cc_final: 0.6538 (mpp) REVERT: B 33 VAL cc_start: 0.8397 (t) cc_final: 0.7837 (t) REVERT: B 84 MET cc_start: 0.8955 (tmm) cc_final: 0.8677 (tmm) REVERT: B 797 THR cc_start: 0.8177 (p) cc_final: 0.7892 (t) REVERT: B 939 MET cc_start: 0.8047 (tpt) cc_final: 0.7751 (tpp) REVERT: C 84 MET cc_start: 0.6246 (mmm) cc_final: 0.5918 (mmm) REVERT: E 16 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7193 (mpt180) REVERT: E 34 MET cc_start: 0.8092 (tpp) cc_final: 0.7717 (ttm) REVERT: E 83 MET cc_start: 0.7020 (mpp) cc_final: 0.5821 (tpp) REVERT: E 86 LEU cc_start: 0.6222 (tt) cc_final: 0.5553 (pp) REVERT: G 163 PRO cc_start: 0.6052 (OUTLIER) cc_final: 0.5825 (Cg_endo) REVERT: H 7 MET cc_start: 0.4295 (tmm) cc_final: 0.3180 (mpp) REVERT: I 74 ASN cc_start: 0.8804 (m-40) cc_final: 0.8568 (t0) outliers start: 4 outliers final: 0 residues processed: 189 average time/residue: 0.4776 time to fit residues: 149.0069 Evaluate side-chains 131 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 421 optimal weight: 0.0870 chunk 320 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 428 optimal weight: 40.0000 chunk 453 optimal weight: 30.0000 chunk 223 optimal weight: 0.5980 chunk 405 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 overall best weight: 4.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 277 ASN A 280 GLN A 627 GLN A 670 HIS ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 719 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN I 180 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 35513 Z= 0.320 Angle : 0.741 11.370 48404 Z= 0.397 Chirality : 0.048 0.422 5615 Planarity : 0.005 0.140 6304 Dihedral : 5.516 41.602 5052 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.65 % Favored : 94.05 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 4679 helix: 1.09 (0.18), residues: 799 sheet: 0.52 (0.14), residues: 1297 loop : -1.11 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 253 HIS 0.012 0.002 HIS A1138 PHE 0.027 0.002 PHE C 281 TYR 0.028 0.003 TYR C 642 ARG 0.010 0.001 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 MET cc_start: 0.7376 (tpp) cc_final: 0.6957 (mmm) REVERT: A 641 TYR cc_start: 0.4656 (p90) cc_final: 0.3974 (p90) REVERT: A 913 MET cc_start: 0.7347 (mpp) cc_final: 0.6836 (mpp) REVERT: C 84 MET cc_start: 0.6604 (mmm) cc_final: 0.6374 (mmm) REVERT: E 16 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7255 (mpt180) REVERT: E 34 MET cc_start: 0.8343 (tpp) cc_final: 0.7975 (ttm) REVERT: E 83 MET cc_start: 0.6934 (mpp) cc_final: 0.5595 (ttm) REVERT: E 86 LEU cc_start: 0.6361 (tt) cc_final: 0.5700 (pp) REVERT: G 68 PHE cc_start: 0.6938 (m-80) cc_final: 0.6558 (m-80) REVERT: G 89 GLU cc_start: 0.7645 (pm20) cc_final: 0.7038 (pm20) REVERT: G 163 PRO cc_start: 0.6421 (OUTLIER) cc_final: 0.6199 (Cg_endo) outliers start: 5 outliers final: 1 residues processed: 180 average time/residue: 0.4664 time to fit residues: 141.4612 Evaluate side-chains 123 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 377 optimal weight: 40.0000 chunk 257 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 chunk 187 optimal weight: 0.0020 chunk 386 optimal weight: 9.9990 chunk 313 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 231 optimal weight: 0.1980 chunk 406 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 3.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 522 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 627 GLN B 733 GLN B 833 GLN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 719 ASN C 842 GLN ** C 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN C1066 GLN F 6 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35513 Z= 0.210 Angle : 0.615 10.072 48404 Z= 0.326 Chirality : 0.044 0.255 5615 Planarity : 0.004 0.142 6304 Dihedral : 5.155 46.435 5052 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.52 % Favored : 94.18 % Rotamer: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4679 helix: 1.59 (0.18), residues: 787 sheet: 0.39 (0.14), residues: 1286 loop : -1.09 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 120 HIS 0.006 0.001 HIS C 766 PHE 0.017 0.002 PHE C 723 TYR 0.032 0.002 TYR H 145 ARG 0.006 0.001 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TYR cc_start: 0.4585 (p90) cc_final: 0.4101 (p90) REVERT: A 913 MET cc_start: 0.7517 (mpp) cc_final: 0.6853 (mpp) REVERT: B 509 ASP cc_start: 0.7083 (m-30) cc_final: 0.6820 (m-30) REVERT: B 906 MET cc_start: 0.1549 (mtt) cc_final: 0.1251 (mtt) REVERT: E 16 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7297 (mpt180) REVERT: E 34 MET cc_start: 0.8252 (tpp) cc_final: 0.7873 (ttm) REVERT: E 83 MET cc_start: 0.6901 (mpp) cc_final: 0.5609 (ttm) REVERT: E 86 LEU cc_start: 0.6314 (tt) cc_final: 0.5641 (pp) REVERT: G 68 PHE cc_start: 0.6958 (m-80) cc_final: 0.6573 (m-80) REVERT: G 163 PRO cc_start: 0.6362 (OUTLIER) cc_final: 0.6106 (Cg_endo) REVERT: H 111 ILE cc_start: 0.6976 (mp) cc_final: 0.6342 (mm) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.4672 time to fit residues: 131.4370 Evaluate side-chains 127 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 152 optimal weight: 0.9990 chunk 408 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 453 optimal weight: 9.9990 chunk 376 optimal weight: 40.0000 chunk 210 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 568 GLN F 6 GLN F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35513 Z= 0.211 Angle : 0.613 12.171 48404 Z= 0.322 Chirality : 0.044 0.292 5615 Planarity : 0.004 0.138 6304 Dihedral : 5.132 44.459 5052 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4679 helix: 1.61 (0.18), residues: 795 sheet: 0.30 (0.14), residues: 1302 loop : -1.12 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 120 HIS 0.019 0.001 HIS A1138 PHE 0.015 0.002 PHE E 29 TYR 0.025 0.002 TYR H 145 ARG 0.015 0.001 ARG B1057 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.5891 (ptp) cc_final: 0.5548 (ptt) REVERT: A 563 MET cc_start: 0.7573 (tpp) cc_final: 0.6885 (tpt) REVERT: A 641 TYR cc_start: 0.4742 (p90) cc_final: 0.4258 (p90) REVERT: A 1160 ASN cc_start: 0.7724 (m-40) cc_final: 0.7200 (p0) REVERT: B 216 ASP cc_start: 0.8307 (t0) cc_final: 0.8103 (t0) REVERT: B 509 ASP cc_start: 0.7176 (m-30) cc_final: 0.6920 (m-30) REVERT: B 906 MET cc_start: 0.1708 (mtt) cc_final: 0.1302 (mtt) REVERT: C 161 MET cc_start: 0.7717 (tpt) cc_final: 0.7497 (tpp) REVERT: E 16 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7307 (mpt180) REVERT: E 83 MET cc_start: 0.6882 (mpp) cc_final: 0.5614 (ttm) REVERT: E 86 LEU cc_start: 0.6320 (tt) cc_final: 0.5640 (pp) REVERT: G 163 PRO cc_start: 0.6575 (OUTLIER) cc_final: 0.6322 (Cg_endo) REVERT: H 111 ILE cc_start: 0.7001 (mp) cc_final: 0.6417 (mm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.4591 time to fit residues: 130.8993 Evaluate side-chains 131 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 437 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 452 optimal weight: 20.0000 chunk 282 optimal weight: 0.7980 chunk 275 optimal weight: 30.0000 chunk 208 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 719 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35513 Z= 0.233 Angle : 0.632 11.433 48404 Z= 0.335 Chirality : 0.044 0.291 5615 Planarity : 0.004 0.145 6304 Dihedral : 5.271 45.117 5052 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.40 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4679 helix: 1.52 (0.19), residues: 786 sheet: 0.26 (0.15), residues: 1288 loop : -1.24 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 44 HIS 0.011 0.001 HIS A1138 PHE 0.016 0.002 PHE C 630 TYR 0.023 0.002 TYR H 145 ARG 0.011 0.001 ARG B1057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.6833 (p) cc_final: 0.6573 (m) REVERT: A 452 MET cc_start: 0.6283 (ptp) cc_final: 0.5889 (ptt) REVERT: A 563 MET cc_start: 0.7551 (tpp) cc_final: 0.6932 (tpt) REVERT: A 913 MET cc_start: 0.7790 (mpp) cc_final: 0.7220 (mpp) REVERT: B 216 ASP cc_start: 0.8394 (t0) cc_final: 0.8190 (t0) REVERT: B 509 ASP cc_start: 0.7428 (m-30) cc_final: 0.7145 (m-30) REVERT: B 906 MET cc_start: 0.2127 (mtt) cc_final: 0.1638 (mtt) REVERT: E 16 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7512 (mpt180) REVERT: E 34 MET cc_start: 0.8381 (tpp) cc_final: 0.7937 (ttm) REVERT: E 83 MET cc_start: 0.6979 (mpp) cc_final: 0.5714 (ttm) REVERT: E 86 LEU cc_start: 0.6098 (tt) cc_final: 0.5382 (pp) REVERT: F 154 LYS cc_start: 0.5883 (pttt) cc_final: 0.5589 (ttpp) REVERT: H 111 ILE cc_start: 0.6997 (mp) cc_final: 0.6413 (mm) REVERT: I 215 ASN cc_start: 0.7085 (t0) cc_final: 0.6833 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.4754 time to fit residues: 133.0951 Evaluate side-chains 125 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 279 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 42 optimal weight: 0.0670 chunk 355 optimal weight: 40.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 568 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN F 105 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35513 Z= 0.194 Angle : 0.610 9.726 48404 Z= 0.319 Chirality : 0.044 0.240 5615 Planarity : 0.004 0.118 6304 Dihedral : 5.161 45.971 5052 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.99 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4679 helix: 1.67 (0.19), residues: 789 sheet: 0.32 (0.15), residues: 1281 loop : -1.28 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1184 HIS 0.008 0.001 HIS A1138 PHE 0.019 0.001 PHE C 266 TYR 0.021 0.002 TYR H 145 ARG 0.008 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.6195 (ptp) cc_final: 0.5788 (ptt) REVERT: A 563 MET cc_start: 0.7488 (tpp) cc_final: 0.7099 (tpt) REVERT: A 913 MET cc_start: 0.7922 (mpp) cc_final: 0.7042 (mpp) REVERT: B 216 ASP cc_start: 0.8450 (t0) cc_final: 0.8226 (t0) REVERT: B 686 MET cc_start: 0.7213 (ptm) cc_final: 0.6856 (ptm) REVERT: B 694 ARG cc_start: 0.6896 (tpm170) cc_final: 0.6533 (tpm170) REVERT: B 906 MET cc_start: 0.2177 (mtt) cc_final: 0.1728 (mtt) REVERT: E 16 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7575 (mpt180) REVERT: E 83 MET cc_start: 0.6786 (mpp) cc_final: 0.5531 (ttm) REVERT: E 86 LEU cc_start: 0.6236 (tt) cc_final: 0.5463 (pp) REVERT: F 154 LYS cc_start: 0.5819 (pttt) cc_final: 0.5538 (ttpp) REVERT: H 111 ILE cc_start: 0.6948 (mp) cc_final: 0.6423 (mm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4691 time to fit residues: 125.0308 Evaluate side-chains 123 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 411 optimal weight: 8.9990 chunk 433 optimal weight: 8.9990 chunk 395 optimal weight: 4.9990 chunk 421 optimal weight: 30.0000 chunk 432 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 330 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 398 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 719 ASN C 999 ASN C1066 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 35513 Z= 0.323 Angle : 0.717 11.520 48404 Z= 0.383 Chirality : 0.046 0.268 5615 Planarity : 0.005 0.104 6304 Dihedral : 5.775 40.707 5052 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.94 % Favored : 91.76 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4679 helix: 1.09 (0.18), residues: 782 sheet: -0.13 (0.15), residues: 1310 loop : -1.42 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 120 HIS 0.013 0.002 HIS I 216 PHE 0.027 0.002 PHE C 630 TYR 0.035 0.002 TYR G 105 ARG 0.021 0.001 ARG B1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.6545 (ptp) cc_final: 0.6109 (ptt) REVERT: A 563 MET cc_start: 0.7445 (tpp) cc_final: 0.7133 (tpt) REVERT: A 913 MET cc_start: 0.8046 (mpp) cc_final: 0.7187 (mpp) REVERT: B 148 MET cc_start: 0.7710 (tpp) cc_final: 0.7482 (tpp) REVERT: B 343 ASP cc_start: 0.7912 (p0) cc_final: 0.7477 (p0) REVERT: B 906 MET cc_start: 0.2641 (mtt) cc_final: 0.2086 (mtt) REVERT: C 563 MET cc_start: 0.5609 (mmt) cc_final: 0.4662 (tpp) REVERT: E 16 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7578 (mpt180) REVERT: E 83 MET cc_start: 0.6896 (mpp) cc_final: 0.5556 (ttm) REVERT: E 86 LEU cc_start: 0.6191 (tt) cc_final: 0.5457 (pp) REVERT: F 154 LYS cc_start: 0.5811 (pttt) cc_final: 0.5525 (ttpp) REVERT: G 163 PRO cc_start: 0.6899 (OUTLIER) cc_final: 0.6675 (Cg_endo) REVERT: H 111 ILE cc_start: 0.6594 (mp) cc_final: 0.5870 (mm) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.4546 time to fit residues: 113.2840 Evaluate side-chains 114 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 419 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 445 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 467 optimal weight: 30.0000 chunk 430 optimal weight: 9.9990 chunk 372 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 287 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35513 Z= 0.207 Angle : 0.634 10.885 48404 Z= 0.333 Chirality : 0.045 0.257 5615 Planarity : 0.004 0.138 6304 Dihedral : 5.494 45.563 5052 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.38 % Favored : 93.30 % 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 : 0.48 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4679 helix: 1.48 (0.19), residues: 788 sheet: -0.10 (0.14), residues: 1318 loop : -1.44 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 120 HIS 0.008 0.001 HIS A 208 PHE 0.026 0.002 PHE C 101 TYR 0.061 0.002 TYR B 641 ARG 0.010 0.001 ARG B 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7238 (tpt) cc_final: 0.6730 (tpt) REVERT: A 452 MET cc_start: 0.6419 (ptp) cc_final: 0.6037 (ptt) REVERT: A 563 MET cc_start: 0.7322 (tpp) cc_final: 0.7070 (tpt) REVERT: A 913 MET cc_start: 0.8029 (mpp) cc_final: 0.7213 (mpp) REVERT: B 148 MET cc_start: 0.7807 (tpp) cc_final: 0.7315 (ttm) REVERT: B 686 MET cc_start: 0.7622 (ptm) cc_final: 0.7302 (ptm) REVERT: B 906 MET cc_start: 0.2615 (mtt) cc_final: 0.2170 (mtt) REVERT: C 563 MET cc_start: 0.5873 (mmt) cc_final: 0.4955 (tpp) REVERT: E 16 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7572 (mpt180) REVERT: E 83 MET cc_start: 0.6777 (mpp) cc_final: 0.5529 (ttm) REVERT: E 86 LEU cc_start: 0.5965 (tt) cc_final: 0.5320 (pp) REVERT: F 154 LYS cc_start: 0.5684 (pttt) cc_final: 0.5385 (ttpp) REVERT: H 111 ILE cc_start: 0.6764 (mp) cc_final: 0.6170 (mm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4732 time to fit residues: 121.0542 Evaluate side-chains 119 residues out of total 4083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 228 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 396 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 377 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.078661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055388 restraints weight = 540926.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.053739 restraints weight = 408667.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053663 restraints weight = 375653.783| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35513 Z= 0.274 Angle : 0.685 10.738 48404 Z= 0.363 Chirality : 0.046 0.260 5615 Planarity : 0.005 0.119 6304 Dihedral : 5.786 42.309 5052 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.50 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.02 (0.12), residues: 4679 helix: 1.22 (0.18), residues: 779 sheet: -0.29 (0.14), residues: 1319 loop : -1.53 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 120 HIS 0.008 0.002 HIS A1138 PHE 0.027 0.002 PHE A 850 TYR 0.056 0.002 TYR B 641 ARG 0.013 0.001 ARG B 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5905.17 seconds wall clock time: 110 minutes 16.83 seconds (6616.83 seconds total)