Starting phenix.real_space_refine on Tue Apr 16 06:39:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xst_33434/04_2024/7xst_33434_neut.pdb" } resolution = 3.04 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4632 atoms to isotropic. 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 138 5.16 5 C 21277 2.51 5 N 5572 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "N GLU 1": "OE1" <-> "OE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "J GLU 1": "OE1" <-> "OE2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "D GLU 1": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F GLU 1": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33532 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7633 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 55, 'TRANS': 954} Chain breaks: 11 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 7611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7611 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 55, 'TRANS': 953} Chain breaks: 11 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7638 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 55, 'TRANS': 952} Chain breaks: 11 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "L" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 874 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 943 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 872 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 943 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 874 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 943 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.53, per 1000 atoms: 0.43 Number of scatterers: 33532 At special positions: 0 Unit cell: (184.3, 165.87, 218.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 6545 8.00 N 5572 7.00 C 21277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.07 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.09 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.86 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.18 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.18 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.18 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 282 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 282 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1134 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 282 " Time building additional restraints: 13.16 Conformation dependent library (CDL) restraints added in 6.2 seconds 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 82 sheets defined 18.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.629A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.732A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.687A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.659A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 removed outlier: 3.886A pdb=" N ASN A 450 " --> pdb=" O GLY A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.772A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.502A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 880 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.501A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.704A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.507A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.519A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.556A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.783A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.732A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.688A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.660A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 removed outlier: 3.886A pdb=" N ASN B 450 " --> pdb=" O GLY B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.469A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.554A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.520A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.671A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.537A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.531A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.209A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.584A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.733A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.687A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.659A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 450 removed outlier: 3.885A pdb=" N ASN C 450 " --> pdb=" O GLY C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 450' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.909A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.787A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.591A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.702A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 890 removed outlier: 4.079A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.929A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.801A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.452A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.140A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.501A pdb=" N ASP L 89 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 86 through 90' Processing helix chain 'M' and resid 55 through 59 removed outlier: 4.611A pdb=" N GLY M 58 " --> pdb=" O ARG M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.501A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'I' and resid 55 through 59 removed outlier: 4.611A pdb=" N GLY I 58 " --> pdb=" O ARG I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.565A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 removed outlier: 4.612A pdb=" N GLY E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.776A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.198A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.198A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.930A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.541A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 279 removed outlier: 7.330A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.711A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.508A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 541 removed outlier: 5.487A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.437A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.199A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.199A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.541A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.329A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.762A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.508A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 542 removed outlier: 3.655A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.831A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.376A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.053A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.198A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.198A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.541A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 278 through 279 removed outlier: 7.330A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.953A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.508A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.078A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.675A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.367A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.598A pdb=" N PHE L 106 " --> pdb=" O ARG L 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.866A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.866A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AG2, first strand: chain 'N' and resid 18 through 22 Processing sheet with id=AG3, first strand: chain 'N' and resid 45 through 50 removed outlier: 6.751A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 117 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA O 12 " --> pdb=" O THR O 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA O 12 " --> pdb=" O THR O 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.366A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.598A pdb=" N PHE H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.866A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.866A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AH5, first strand: chain 'J' and resid 45 through 50 removed outlier: 6.752A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 117 " --> pdb=" O TYR J 94 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AH9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AI1, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.367A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.597A pdb=" N PHE D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.865A pdb=" N VAL E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.865A pdb=" N VAL E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AI6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AI7, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.751A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 117 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.717A pdb=" N ALA G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 18 through 23 1304 hydrogen bonds defined for protein. 3399 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: 19.89 Time building geometry restraints manager: 14.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5510 1.26 - 1.40: 8723 1.40 - 1.54: 19715 1.54 - 1.68: 177 1.68 - 1.82: 171 Bond restraints: 34296 Sorted by residual: bond pdb=" N PRO M 45 " pdb=" CD PRO M 45 " ideal model delta sigma weight residual 1.473 1.187 0.286 1.40e-02 5.10e+03 4.16e+02 bond pdb=" N PRO C 897 " pdb=" CD PRO C 897 " ideal model delta sigma weight residual 1.473 1.294 0.179 1.40e-02 5.10e+03 1.64e+02 bond pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 1.473 1.302 0.171 1.40e-02 5.10e+03 1.50e+02 bond pdb=" C PRO B 897 " pdb=" O PRO B 897 " ideal model delta sigma weight residual 1.233 1.116 0.117 1.16e-02 7.43e+03 1.01e+02 bond pdb=" C PRO C 897 " pdb=" O PRO C 897 " ideal model delta sigma weight residual 1.233 1.127 0.106 1.16e-02 7.43e+03 8.36e+01 ... (remaining 34291 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.92: 581 103.92 - 111.51: 14905 111.51 - 119.10: 12862 119.10 - 126.69: 18000 126.69 - 134.28: 423 Bond angle restraints: 46771 Sorted by residual: angle pdb=" CA PHE A1121 " pdb=" CB PHE A1121 " pdb=" CG PHE A1121 " ideal model delta sigma weight residual 113.80 124.18 -10.38 1.00e+00 1.00e+00 1.08e+02 angle pdb=" C THR C 599 " pdb=" CA THR C 599 " pdb=" CB THR C 599 " ideal model delta sigma weight residual 109.42 97.01 12.41 1.35e+00 5.49e-01 8.46e+01 angle pdb=" C PRO A 322 " pdb=" CA PRO A 322 " pdb=" CB PRO A 322 " ideal model delta sigma weight residual 111.11 101.13 9.98 1.17e+00 7.31e-01 7.27e+01 angle pdb=" N VAL B 503 " pdb=" CA VAL B 503 " pdb=" C VAL B 503 " ideal model delta sigma weight residual 112.29 104.89 7.40 9.40e-01 1.13e+00 6.20e+01 angle pdb=" N VAL C 503 " pdb=" CA VAL C 503 " pdb=" C VAL C 503 " ideal model delta sigma weight residual 112.29 104.89 7.40 9.40e-01 1.13e+00 6.19e+01 ... (remaining 46766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 18901 17.83 - 35.65: 1355 35.65 - 53.48: 230 53.48 - 71.30: 71 71.30 - 89.13: 23 Dihedral angle restraints: 20580 sinusoidal: 7916 harmonic: 12664 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -17.55 -68.45 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.02 67.02 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" C GLN B1071 " pdb=" N GLN B1071 " pdb=" CA GLN B1071 " pdb=" CB GLN B1071 " ideal model delta harmonic sigma weight residual -122.60 -140.14 17.54 0 2.50e+00 1.60e-01 4.92e+01 ... (remaining 20577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4990 0.140 - 0.280: 315 0.280 - 0.420: 63 0.420 - 0.561: 9 0.561 - 0.701: 4 Chirality restraints: 5381 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA GLN B1071 " pdb=" N GLN B1071 " pdb=" C GLN B1071 " pdb=" CB GLN B1071 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 5378 not shown) Planarity restraints: 6079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " -0.348 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG C1311 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.348 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG A1310 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.327 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG B1308 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.491 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.073 2.00e-02 2.50e+03 ... (remaining 6076 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4358 2.75 - 3.29: 31642 3.29 - 3.82: 51370 3.82 - 4.36: 63237 4.36 - 4.90: 111321 Nonbonded interactions: 261928 Sorted by model distance: nonbonded pdb=" O ASP G 52 " pdb=" OG SER G 66 " model vdw 2.211 2.440 nonbonded pdb=" O ASP O 52 " pdb=" OG SER O 66 " model vdw 2.211 2.440 nonbonded pdb=" O ASP K 52 " pdb=" OG SER K 66 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP C 442 " pdb=" NE ARG C 509 " model vdw 2.250 2.520 nonbonded pdb=" OD2 ASP A 442 " pdb=" NE ARG A 509 " model vdw 2.250 2.520 ... (remaining 261923 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 27 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 318 or (resid 3 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 320 through \ 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) or r \ esid 555 or (resid 556 through 559 and (name N or name CA or name C or name O or \ name CB )) or resid 560 through 563 or (resid 564 and (name N or name CA or nam \ e C or name O or name CB )) or resid 565 through 570 or (resid 571 through 572 a \ nd (name N or name CA or name C or name O or name CB )) or resid 573 through 614 \ or (resid 615 and (name N or name CA or name C or name O or name CB )) or resid \ 616 through 619 or resid 641 through 676 or (resid 690 and (name N or name CA o \ r name C or name O or name CB )) or resid 691 through 710 or (resid 711 and (nam \ e N or name CA or name C or name O or name CB )) or resid 712 through 747 or (re \ sid 748 and (name N or name CA or name C or name O or name CB )) or resid 749 th \ rough 758 or (resid 759 and (name N or name CA or name C or name O or name CB )) \ or resid 760 through 790 or (resid 791 and (name N or name CA or name C or name \ O or name CB )) or resid 792 through 827 or (resid 828 and (name N or name CA o \ r name C or name O or name CB )) or resid 855 through 984 or (resid 985 and (nam \ e N or name CA or name C or name O or name CB )) or resid 986 through 987 or (re \ sid 988 through 989 and (name N or name CA or name C or name O or name CB )) or \ resid 990 through 993 or (resid 994 and (name N or name CA or name C or name O o \ r name CB )) or resid 995 through 1030 or (resid 1031 and (name N or name CA or \ name C or name O or name CB )) or resid 1032 through 1037 or (resid 1038 and (na \ me N or name CA or name C or name O or name CB )) or resid 1039 through 1050 or \ (resid 1051 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 52 through 1110 or (resid 1111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1112 through 1122 or (resid 1123 and (name N or name CA or name \ C or name O or name CB )) or resid 1124 through 1138 or (resid 1139 and (name N \ or name CA or name C or name O or name CB )) or resid 1140 through 1143 or (res \ id 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or \ resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 230 or (resid 231 and (name N o \ r name CA or name C or name O or name CB )) or resid 232 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 555 or (res \ id 556 through 559 and (name N or name CA or name C or name O or name CB )) or r \ esid 560 through 563 or (resid 564 and (name N or name CA or name C or name O or \ name CB )) or resid 565 through 570 or (resid 571 through 572 and (name N or na \ me CA or name C or name O or name CB )) or resid 573 through 619 or resid 641 th \ rough 676 or (resid 690 and (name N or name CA or name C or name O or name CB )) \ or resid 691 through 704 or (resid 705 through 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 747 or (resid 748 and (name N \ or name CA or name C or name O or name CB )) or resid 749 through 790 or (resid \ 791 and (name N or name CA or name C or name O or name CB )) or resid 792 throug \ h 827 or (resid 828 and (name N or name CA or name C or name O or name CB )) or \ resid 855 through 984 or (resid 985 and (name N or name CA or name C or name O o \ r name CB )) or resid 986 through 987 or (resid 988 through 989 and (name N or n \ ame CA or name C or name O or name CB )) or resid 990 through 1037 or (resid 103 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1039 through \ 1050 or (resid 1051 and (name N or name CA or name C or name O or name CB )) or \ resid 1052 through 1085 or (resid 1086 through 1087 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1088 through 1103 or (resid 1104 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1105 through 1110 or ( \ resid 1111 and (name N or name CA or name C or name O or name CB )) or resid 111 \ 2 through 1122 or (resid 1123 and (name N or name CA or name C or name O or name \ CB )) or resid 1124 through 1143 or (resid 1144 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 114 or (resid 115 and (name N or n \ ame CA or name C or name O or name CB )) or resid 116 through 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB )) or resid 232 through 31 \ 4 or (resid 315 and (name N or name CA or name C or name O or name CB )) or resi \ d 316 through 318 or (resid 319 and (name N or name CA or name C or name O or na \ me CB )) or resid 320 through 556 or (resid 557 through 559 and (name N or name \ CA or name C or name O or name CB )) or resid 560 through 568 or (resid 569 thro \ ugh 572 and (name N or name CA or name C or name O or name CB )) or resid 573 th \ rough 614 or (resid 615 and (name N or name CA or name C or name O or name CB )) \ or resid 616 through 619 or resid 641 through 662 or (resid 663 and (name N or \ name CA or name C or name O or name CB )) or resid 664 through 701 or (resid 702 \ and (name N or name CA or name C or name O or name CB )) or resid 703 through 7 \ 04 or (resid 705 through 706 and (name N or name CA or name C or name O or name \ CB )) or resid 707 through 710 or (resid 711 and (name N or name CA or name C or \ name O or name CB )) or resid 712 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 760 through 794 or (resid 795 and \ (name N or name CA or name C or name O or name CB )) or resid 796 through 807 o \ r (resid 808 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 09 through 818 or (resid 819 and (name N or name CA or name C or name O or name \ CB )) or resid 820 through 824 or (resid 825 and (name N or name CA or name C or \ name O or name CB )) or resid 826 through 917 or (resid 918 and (name N or name \ CA or name C or name O or name CB )) or resid 919 through 946 or (resid 947 and \ (name N or name CA or name C or name O or name CB )) or resid 948 through 963 o \ r (resid 964 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 65 through 993 or (resid 994 and (name N or name CA or name C or name O or name \ CB )) or resid 995 through 1030 or (resid 1031 and (name N or name CA or name C \ or name O or name CB )) or resid 1032 through 1072 or (resid 1073 and (name N or \ name CA or name C or name O or name CB )) or resid 1074 through 1085 or (resid \ 1086 through 1087 and (name N or name CA or name C or name O or name CB )) or re \ sid 1088 through 1103 or (resid 1104 and (name N or name CA or name C or name O \ or name CB )) or resid 1105 through 1137 or (resid 1138 through 1139 and (name N \ or name CA or name C or name O or name CB )) or resid 1140 or (resid 1141 throu \ gh 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 t \ hrough 1145 or (resid 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1301 through 1310)) } ncs_group { reference = (chain 'D' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 117)) selection = chain 'H' selection = (chain 'L' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 117)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.030 Extract box with map and model: 10.240 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 91.030 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 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 : 0.008 0.286 34296 Z= 0.562 Angle : 1.196 12.414 46771 Z= 0.795 Chirality : 0.082 0.701 5381 Planarity : 0.011 0.300 6048 Dihedral : 12.977 89.130 12327 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.08 % Favored : 93.90 % Rotamer: Outliers : 0.46 % Allowed : 2.66 % Favored : 96.88 % Cbeta Deviations : 1.11 % 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: -1.69 (0.12), residues: 4311 helix: 0.33 (0.21), residues: 624 sheet: -1.05 (0.15), residues: 1124 loop : -1.55 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 353 HIS 0.005 0.001 HIS B1058 PHE 0.053 0.002 PHE A1121 TYR 0.039 0.003 TYR B 351 ARG 0.011 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 297 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 756 TYR cc_start: 0.7620 (m-80) cc_final: 0.6909 (m-80) REVERT: A 1125 ASN cc_start: 0.7505 (p0) cc_final: 0.7209 (p0) REVERT: B 209 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7170 (Cg_exo) REVERT: B 298 GLU cc_start: 0.7447 (tt0) cc_final: 0.7203 (tt0) REVERT: C 355 ARG cc_start: 0.0963 (OUTLIER) cc_final: -0.0016 (ttm170) REVERT: C 981 PHE cc_start: 0.8154 (m-80) cc_final: 0.7847 (m-80) REVERT: D 115 VAL cc_start: 0.2645 (t) cc_final: 0.2359 (p) REVERT: E 34 VAL cc_start: 0.3168 (OUTLIER) cc_final: 0.2940 (m) outliers start: 16 outliers final: 5 residues processed: 313 average time/residue: 0.4174 time to fit residues: 221.3231 Evaluate side-chains 194 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 45 PRO Chi-restraints excluded: chain G residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 0.7980 chunk 330 optimal weight: 40.0000 chunk 183 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 341 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 chunk 395 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1071 GLN B1083 HIS C 207 HIS C 271 GLN C 536 ASN C 703 ASN C 907 ASN C 913 GLN C1010 GLN L 81 GLN L 109 GLN M 1 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN I 1 GLN D 81 GLN D 109 GLN E 1 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34296 Z= 0.197 Angle : 0.590 9.021 46771 Z= 0.308 Chirality : 0.046 0.356 5381 Planarity : 0.005 0.068 6048 Dihedral : 6.346 57.908 5375 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.37 % Allowed : 6.61 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4311 helix: 1.21 (0.21), residues: 647 sheet: -0.76 (0.14), residues: 1211 loop : -1.17 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.025 0.001 PHE C 906 TYR 0.023 0.001 TYR B 170 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1125 ASN cc_start: 0.7387 (p0) cc_final: 0.7090 (p0) REVERT: B 314 GLN cc_start: 0.7902 (tt0) cc_final: 0.7639 (tp40) REVERT: B 954 HIS cc_start: 0.7813 (m90) cc_final: 0.7612 (m-70) REVERT: C 355 ARG cc_start: 0.0837 (OUTLIER) cc_final: -0.0520 (ttt180) REVERT: C 697 MET cc_start: 0.8237 (mtp) cc_final: 0.8001 (mtp) REVERT: C 981 PHE cc_start: 0.8135 (m-80) cc_final: 0.7766 (m-80) REVERT: H 34 MET cc_start: 0.2060 (mmp) cc_final: 0.1371 (mtp) REVERT: J 83 MET cc_start: -0.0036 (mpp) cc_final: -0.0553 (mtt) REVERT: D 115 VAL cc_start: 0.2953 (t) cc_final: 0.2644 (p) REVERT: F 83 MET cc_start: 0.2441 (pmm) cc_final: 0.1938 (mtp) outliers start: 48 outliers final: 24 residues processed: 248 average time/residue: 0.4227 time to fit residues: 182.8054 Evaluate side-chains 201 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 50.0000 chunk 122 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 269 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 396 optimal weight: 20.0000 chunk 428 optimal weight: 40.0000 chunk 353 optimal weight: 30.0000 chunk 393 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 chunk 318 optimal weight: 30.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 314 GLN A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 564 GLN B 804 GLN B 824 ASN C 87 ASN C 164 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 317 ASN C 913 GLN C 955 ASN M 31 ASN N 77 ASN O 6 GLN H 39 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.215 34296 Z= 1.436 Angle : 1.190 15.030 46771 Z= 0.621 Chirality : 0.080 0.567 5381 Planarity : 0.009 0.087 6048 Dihedral : 7.989 59.497 5366 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.50 % Rotamer: Outliers : 3.81 % Allowed : 10.02 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4311 helix: -0.96 (0.18), residues: 643 sheet: -0.89 (0.15), residues: 1206 loop : -1.58 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 104 HIS 0.018 0.004 HIS B1058 PHE 0.052 0.005 PHE A 855 TYR 0.040 0.004 TYR B 266 ARG 0.028 0.002 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 168 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 994 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7004 (t0) REVERT: B 314 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 591 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 895 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: B 1041 ASP cc_start: 0.6936 (t0) cc_final: 0.6695 (t0) REVERT: B 1115 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 287 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (t0) REVERT: C 960 ASN cc_start: 0.8041 (t0) cc_final: 0.7630 (m-40) REVERT: C 981 PHE cc_start: 0.7997 (m-80) cc_final: 0.7658 (m-80) REVERT: C 1139 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7615 (p0) REVERT: H 34 MET cc_start: 0.2343 (mmp) cc_final: 0.1651 (mtp) REVERT: D 115 VAL cc_start: 0.3127 (t) cc_final: 0.2811 (p) REVERT: E 34 VAL cc_start: 0.3222 (OUTLIER) cc_final: 0.2890 (m) outliers start: 133 outliers final: 93 residues processed: 281 average time/residue: 0.3966 time to fit residues: 197.0036 Evaluate side-chains 260 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 158 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 398 optimal weight: 40.0000 chunk 421 optimal weight: 40.0000 chunk 207 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 207 HIS B 564 GLN C 164 ASN C 913 GLN H 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34296 Z= 0.290 Angle : 0.604 9.257 46771 Z= 0.317 Chirality : 0.047 0.371 5381 Planarity : 0.005 0.061 6048 Dihedral : 6.376 58.536 5362 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.12 % Allowed : 12.05 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4311 helix: 0.33 (0.20), residues: 659 sheet: -0.54 (0.15), residues: 1204 loop : -1.30 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 258 HIS 0.004 0.001 HIS F 35 PHE 0.026 0.002 PHE C 565 TYR 0.024 0.001 TYR B 170 ARG 0.006 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7594 (mm) cc_final: 0.7391 (mt) REVERT: C 660 TYR cc_start: 0.8891 (m-80) cc_final: 0.8686 (m-80) REVERT: C 895 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: C 902 MET cc_start: 0.8407 (mmt) cc_final: 0.8129 (tpt) REVERT: C 960 ASN cc_start: 0.7817 (t0) cc_final: 0.7391 (m-40) REVERT: H 34 MET cc_start: 0.2173 (mmp) cc_final: 0.1438 (mtp) REVERT: H 82 MET cc_start: 0.0910 (mtt) cc_final: 0.0449 (mpp) REVERT: D 115 VAL cc_start: 0.3288 (t) cc_final: 0.2992 (p) REVERT: E 34 VAL cc_start: 0.3421 (OUTLIER) cc_final: 0.3108 (m) outliers start: 74 outliers final: 39 residues processed: 239 average time/residue: 0.4380 time to fit residues: 187.5450 Evaluate side-chains 207 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 359 optimal weight: 50.0000 chunk 291 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 378 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 314 GLN A 334 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 271 GLN C 913 GLN F 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 34296 Z= 0.442 Angle : 0.650 9.842 46771 Z= 0.337 Chirality : 0.049 0.401 5381 Planarity : 0.005 0.059 6048 Dihedral : 6.091 56.433 5361 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.66 % Allowed : 12.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4311 helix: 0.32 (0.20), residues: 666 sheet: -0.41 (0.15), residues: 1214 loop : -1.27 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 92 HIS 0.008 0.001 HIS B1058 PHE 0.023 0.002 PHE A 823 TYR 0.042 0.002 TYR B 204 ARG 0.005 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 173 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.6444 (ptp-170) REVERT: B 965 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7815 (mt0) REVERT: B 1039 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8215 (mtp180) REVERT: C 895 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: C 902 MET cc_start: 0.8367 (mmt) cc_final: 0.8038 (tpt) REVERT: C 960 ASN cc_start: 0.7904 (t0) cc_final: 0.7465 (m-40) REVERT: D 115 VAL cc_start: 0.3300 (t) cc_final: 0.2932 (p) REVERT: E 34 VAL cc_start: 0.3289 (OUTLIER) cc_final: 0.2984 (m) outliers start: 93 outliers final: 72 residues processed: 244 average time/residue: 0.3952 time to fit residues: 169.5457 Evaluate side-chains 235 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 160 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1057 PRO Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 0.9990 chunk 379 optimal weight: 40.0000 chunk 83 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 421 optimal weight: 30.0000 chunk 350 optimal weight: 30.0000 chunk 195 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 221 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 207 HIS B 564 GLN C 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34296 Z= 0.192 Angle : 0.526 9.726 46771 Z= 0.275 Chirality : 0.045 0.364 5381 Planarity : 0.004 0.056 6048 Dihedral : 5.443 57.248 5361 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.38 % Allowed : 13.82 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4311 helix: 0.92 (0.20), residues: 667 sheet: -0.30 (0.15), residues: 1245 loop : -1.08 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 92 HIS 0.004 0.001 HIS F 35 PHE 0.017 0.001 PHE C 65 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 170 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 954 HIS cc_start: 0.7980 (m90) cc_final: 0.7758 (m-70) REVERT: C 714 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8537 (mm) REVERT: C 895 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: C 902 MET cc_start: 0.8384 (mmt) cc_final: 0.8114 (tpt) REVERT: C 960 ASN cc_start: 0.7835 (t0) cc_final: 0.7425 (m-40) REVERT: N 83 MET cc_start: 0.1084 (mmt) cc_final: 0.0738 (mmm) REVERT: D 115 VAL cc_start: 0.3158 (t) cc_final: 0.2807 (p) outliers start: 83 outliers final: 55 residues processed: 228 average time/residue: 0.4036 time to fit residues: 162.5215 Evaluate side-chains 218 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 240 optimal weight: 30.0000 chunk 308 optimal weight: 20.0000 chunk 238 optimal weight: 40.0000 chunk 355 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 913 GLN M 31 ASN O 94 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 34296 Z= 0.411 Angle : 0.617 9.849 46771 Z= 0.320 Chirality : 0.049 0.397 5381 Planarity : 0.005 0.056 6048 Dihedral : 5.603 56.211 5361 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 13.74 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4311 helix: 0.65 (0.20), residues: 666 sheet: -0.22 (0.15), residues: 1192 loop : -1.13 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 36 HIS 0.008 0.001 HIS B1058 PHE 0.022 0.002 PHE A1121 TYR 0.029 0.002 TYR A 265 ARG 0.006 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 162 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.6820 (ttp-110) cc_final: 0.6363 (ptp-170) REVERT: B 293 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8578 (tp) REVERT: B 1039 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8232 (mtp180) REVERT: C 287 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8004 (t0) REVERT: C 714 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 895 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: C 960 ASN cc_start: 0.7862 (t0) cc_final: 0.7508 (m-40) REVERT: D 115 VAL cc_start: 0.2946 (t) cc_final: 0.2612 (p) outliers start: 104 outliers final: 78 residues processed: 241 average time/residue: 0.4335 time to fit residues: 182.3887 Evaluate side-chains 239 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 156 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 267 optimal weight: 0.7980 chunk 286 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS C 804 GLN C 913 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34296 Z= 0.157 Angle : 0.502 8.237 46771 Z= 0.261 Chirality : 0.044 0.358 5381 Planarity : 0.004 0.055 6048 Dihedral : 5.023 59.597 5361 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.77 % Allowed : 14.51 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4311 helix: 1.24 (0.21), residues: 661 sheet: -0.08 (0.15), residues: 1224 loop : -0.95 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 53 HIS 0.009 0.001 HIS F 35 PHE 0.017 0.001 PHE A 192 TYR 0.023 0.001 TYR A 265 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 173 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.6758 (ttp-110) cc_final: 0.6409 (ptp-170) REVERT: B 954 HIS cc_start: 0.7990 (m90) cc_final: 0.7768 (m-70) REVERT: B 1039 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8017 (mtp180) REVERT: C 869 MET cc_start: 0.9057 (mtt) cc_final: 0.8771 (mtp) REVERT: C 895 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: C 902 MET cc_start: 0.8387 (mmt) cc_final: 0.7857 (tpt) REVERT: C 960 ASN cc_start: 0.7733 (t0) cc_final: 0.7321 (m-40) REVERT: H 82 MET cc_start: 0.0995 (mtt) cc_final: 0.0290 (mpp) REVERT: D 115 VAL cc_start: 0.2807 (t) cc_final: 0.2480 (p) outliers start: 62 outliers final: 48 residues processed: 216 average time/residue: 0.4234 time to fit residues: 158.3268 Evaluate side-chains 214 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 50.0000 chunk 402 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 170 optimal weight: 0.0070 chunk 307 optimal weight: 40.0000 chunk 120 optimal weight: 30.0000 chunk 353 optimal weight: 50.0000 chunk 370 optimal weight: 20.0000 chunk 390 optimal weight: 30.0000 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 30 ASN B 207 HIS C 913 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.119 34296 Z= 0.766 Angle : 0.774 11.594 46771 Z= 0.401 Chirality : 0.058 0.727 5381 Planarity : 0.006 0.077 6048 Dihedral : 6.001 56.130 5361 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.58 % Allowed : 14.14 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 4311 helix: 0.16 (0.20), residues: 667 sheet: -0.29 (0.15), residues: 1202 loop : -1.18 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 53 HIS 0.012 0.002 HIS C1048 PHE 0.034 0.003 PHE A1121 TYR 0.031 0.002 TYR B 204 ARG 0.015 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 164 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 PHE cc_start: 0.7303 (m-80) cc_final: 0.7097 (m-80) REVERT: B 965 GLN cc_start: 0.8090 (mt0) cc_final: 0.7739 (mt0) REVERT: B 1039 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8471 (mtp180) REVERT: C 714 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (mm) REVERT: C 895 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: C 960 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7574 (m-40) REVERT: D 115 VAL cc_start: 0.2864 (t) cc_final: 0.2508 (p) outliers start: 90 outliers final: 77 residues processed: 233 average time/residue: 0.4120 time to fit residues: 168.3094 Evaluate side-chains 238 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 157 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain G residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 5.9990 chunk 414 optimal weight: 0.4980 chunk 252 optimal weight: 0.0170 chunk 196 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 chunk 434 optimal weight: 30.0000 chunk 399 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 271 GLN L 39 GLN M 31 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34296 Z= 0.171 Angle : 0.525 10.445 46771 Z= 0.274 Chirality : 0.045 0.423 5381 Planarity : 0.004 0.055 6048 Dihedral : 5.319 57.664 5361 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.52 % Allowed : 15.14 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4311 helix: 0.98 (0.21), residues: 660 sheet: -0.06 (0.15), residues: 1200 loop : -1.02 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 53 HIS 0.003 0.001 HIS C 207 PHE 0.015 0.001 PHE C1121 TYR 0.020 0.001 TYR B 170 ARG 0.003 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 162 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 954 HIS cc_start: 0.8000 (m90) cc_final: 0.7762 (m-70) REVERT: B 1039 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8046 (mtp180) REVERT: C 895 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: C 902 MET cc_start: 0.8383 (mmt) cc_final: 0.7815 (tpt) REVERT: C 960 ASN cc_start: 0.7838 (t0) cc_final: 0.7432 (m-40) REVERT: H 82 MET cc_start: 0.1141 (mtt) cc_final: 0.0516 (mpp) REVERT: D 115 VAL cc_start: 0.2824 (t) cc_final: 0.2487 (p) outliers start: 53 outliers final: 45 residues processed: 202 average time/residue: 0.4255 time to fit residues: 149.9796 Evaluate side-chains 205 residues out of total 3780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain F residue 16 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 2.9990 chunk 368 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 318 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 346 optimal weight: 0.0070 chunk 144 optimal weight: 40.0000 chunk 355 optimal weight: 7.9990 chunk 43 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 207 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.262725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.213260 restraints weight = 41446.001| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 5.46 r_work: 0.3933 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34296 Z= 0.166 Angle : 0.506 11.863 46771 Z= 0.262 Chirality : 0.044 0.373 5381 Planarity : 0.004 0.054 6048 Dihedral : 4.998 58.785 5361 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.52 % Allowed : 15.14 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4311 helix: 1.26 (0.21), residues: 666 sheet: 0.10 (0.15), residues: 1199 loop : -0.93 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 53 HIS 0.002 0.001 HIS C 207 PHE 0.015 0.001 PHE C1121 TYR 0.019 0.001 TYR B 170 ARG 0.003 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6211.11 seconds wall clock time: 114 minutes 56.64 seconds (6896.64 seconds total)