Starting phenix.real_space_refine on Sat Feb 17 03:33:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xsk_22302/02_2024/6xsk_22302.pdb" } resolution = 3.85 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10866 2.51 5 N 2907 2.21 5 O 3468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 24": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "I ARG 94": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17322 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "E" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1356 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.16, per 1000 atoms: 0.59 Number of scatterers: 17322 At special positions: 0 Unit cell: (125.19, 121.98, 151.94, 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 81 16.00 O 3468 8.00 N 2907 7.00 C 10866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS F 47 " distance=2.01 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.00 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 52 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 52 " 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 21 " " NAG A 403 " - " ASN A 129 " " NAG A 404 " - " ASN A 289 " " NAG B 501 " - " ASN B 154 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 129 " " NAG C 404 " - " ASN C 289 " " NAG D 501 " - " ASN D 154 " " NAG E 401 " - " ASN E 33 " " NAG E 402 " - " ASN E 21 " " NAG E 403 " - " ASN E 289 " " NAG E 404 " - " ASN E 129 " " NAG F 501 " - " ASN F 154 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN A 163 " " NAG O 1 " - " ASN A 63 " " NAG P 1 " - " ASN C 163 " " NAG Q 1 " - " ASN C 95 " " NAG R 1 " - " ASN C 63 " " NAG S 1 " - " ASN E 63 " " NAG T 1 " - " ASN E 95 " " NAG U 1 " - " ASN E 163 " Time building additional restraints: 7.74 Conformation dependent library (CDL) restraints added in 3.4 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 51 sheets defined 20.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.923A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.650A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 75 through 82 removed outlier: 4.208A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 81 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 82 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 4.265A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.632A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.669A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 74 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'J' and resid 79 through 84 removed outlier: 4.470A pdb=" N ALA J 84 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.733A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 84 removed outlier: 4.289A pdb=" N ALA K 84 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.587A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.548A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.519A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 95 " --> pdb=" O CYS H 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS H 33 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.870A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 12 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.088A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.612A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.612A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 235 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.675A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.743A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 168 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 243 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 202 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 204 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.591A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.620A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 12 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.724A pdb=" N VAL C 26 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN C 33 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.517A pdb=" N GLN C 295 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 9.126A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.831A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 268 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.709A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.709A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 235 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.707A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.918A pdb=" N ALA C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD2, first strand: chain 'F' and resid 32 through 33 removed outlier: 3.925A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 12 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.550A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.573A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.462A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 115 through 122 removed outlier: 4.742A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 115 through 122 removed outlier: 4.742A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 229 " --> pdb=" O HIS E 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.575A pdb=" N SER E 146 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER E 138 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLU E 144 " --> pdb=" O SER E 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.923A pdb=" N ALA E 247 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 166 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.675A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.754A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.535A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN J 37 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.981A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.909A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF3, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.565A pdb=" N THR K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR K 49 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.589A pdb=" N GLN I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP I 72 " --> pdb=" O GLN I 77 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 56 through 59 removed outlier: 5.417A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS I 33 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN I 39 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 98 through 99 662 hydrogen bonds defined for protein. 1788 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: 6.09 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4261 1.33 - 1.45: 3923 1.45 - 1.58: 9426 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 17712 Sorted by residual: bond pdb=" N ILE I 97 " pdb=" CA ILE I 97 " ideal model delta sigma weight residual 1.458 1.501 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" N VAL E 36 " pdb=" CA VAL E 36 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N GLN L 89 " pdb=" CA GLN L 89 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N VAL C 34 " pdb=" CA VAL C 34 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.11e-02 8.12e+03 1.10e+01 bond pdb=" N ILE I 99 " pdb=" CA ILE I 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 ... (remaining 17707 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.41: 337 105.41 - 112.62: 9166 112.62 - 119.83: 6260 119.83 - 127.04: 8034 127.04 - 134.25: 233 Bond angle restraints: 24030 Sorted by residual: angle pdb=" C SER E 126 " pdb=" N TRP E 127 " pdb=" CA TRP E 127 " ideal model delta sigma weight residual 123.46 115.19 8.27 1.35e+00 5.49e-01 3.75e+01 angle pdb=" CA VAL C 29 " pdb=" C VAL C 29 " pdb=" O VAL C 29 " ideal model delta sigma weight residual 121.28 114.68 6.60 1.17e+00 7.31e-01 3.18e+01 angle pdb=" C LYS D 127 " pdb=" CA LYS D 127 " pdb=" CB LYS D 127 " ideal model delta sigma weight residual 116.63 110.72 5.91 1.16e+00 7.43e-01 2.59e+01 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 120.82 128.43 -7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C LEU F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta sigma weight residual 120.82 128.35 -7.53 1.50e+00 4.44e-01 2.52e+01 ... (remaining 24025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 10330 21.75 - 43.49: 595 43.49 - 65.24: 76 65.24 - 86.99: 35 86.99 - 108.73: 13 Dihedral angle restraints: 11049 sinusoidal: 4836 harmonic: 6213 Sorted by residual: dihedral pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -174.35 88.35 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 14.18 78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -154.11 68.11 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2083 0.074 - 0.148: 496 0.148 - 0.222: 109 0.222 - 0.296: 26 0.296 - 0.370: 7 Chirality restraints: 2721 Sorted by residual: chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 154 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA VAL A 88 " pdb=" N VAL A 88 " pdb=" C VAL A 88 " pdb=" CB VAL A 88 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA LEU L 33 " pdb=" N LEU L 33 " pdb=" C LEU L 33 " pdb=" CB LEU L 33 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2718 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 401 " -0.254 2.00e-02 2.50e+03 2.16e-01 5.82e+02 pdb=" C7 NAG E 401 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 401 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG E 401 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG E 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 404 " 0.228 2.00e-02 2.50e+03 1.90e-01 4.50e+02 pdb=" C7 NAG E 404 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 404 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG E 404 " -0.312 2.00e-02 2.50e+03 pdb=" O7 NAG E 404 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 501 " 0.182 2.00e-02 2.50e+03 1.50e-01 2.83e+02 pdb=" C7 NAG F 501 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG F 501 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG F 501 " -0.244 2.00e-02 2.50e+03 pdb=" O7 NAG F 501 " -0.020 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4005 2.80 - 3.32: 15286 3.32 - 3.85: 28707 3.85 - 4.37: 32316 4.37 - 4.90: 55228 Nonbonded interactions: 135542 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR A 131 " pdb=" OG1 THR A 155 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.355 2.440 nonbonded pdb=" OG SER A 39 " pdb=" NH2 ARG A 315 " model vdw 2.360 2.520 nonbonded pdb=" OE1 GLU A 175 " pdb=" NH2 ARG A 262 " model vdw 2.366 2.520 ... (remaining 135537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 15.200 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.470 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.006 0.047 17712 Z= 0.424 Angle : 1.057 12.378 24030 Z= 0.687 Chirality : 0.070 0.370 2721 Planarity : 0.008 0.216 3063 Dihedral : 13.846 108.732 6990 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.37 % Allowed : 2.77 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2139 helix: 1.53 (0.27), residues: 372 sheet: 1.30 (0.24), residues: 471 loop : -0.79 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 153 HIS 0.006 0.001 HIS E 130 PHE 0.038 0.002 PHE D 88 TYR 0.046 0.002 TYR J 49 ARG 0.012 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 385 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8545 (mp10) cc_final: 0.8251 (mp10) REVERT: L 32 TRP cc_start: 0.8833 (m-10) cc_final: 0.8153 (m-10) REVERT: L 82 ASP cc_start: 0.8918 (m-30) cc_final: 0.8663 (m-30) REVERT: H 33 CYS cc_start: 0.7487 (m) cc_final: 0.6197 (m) REVERT: H 39 GLN cc_start: 0.9200 (tt0) cc_final: 0.8509 (tm-30) REVERT: H 53 SER cc_start: 0.8908 (m) cc_final: 0.8671 (p) REVERT: H 60 ASN cc_start: 0.9302 (t0) cc_final: 0.8895 (t0) REVERT: H 72 ASP cc_start: 0.9122 (p0) cc_final: 0.8489 (p0) REVERT: H 78 PHE cc_start: 0.7779 (p90) cc_final: 0.7481 (p90) REVERT: H 95 GLU cc_start: 0.8915 (pm20) cc_final: 0.8119 (pm20) REVERT: H 100 ILE cc_start: 0.8643 (tp) cc_final: 0.8205 (tp) REVERT: A 14 CYS cc_start: 0.8833 (m) cc_final: 0.8233 (m) REVERT: A 190 ASP cc_start: 0.8957 (m-30) cc_final: 0.8748 (t0) REVERT: A 225 ASP cc_start: 0.8183 (t70) cc_final: 0.7946 (t0) REVERT: B 37 ASP cc_start: 0.8918 (t0) cc_final: 0.8568 (t0) REVERT: B 77 MET cc_start: 0.9168 (mmm) cc_final: 0.8889 (mmt) REVERT: B 112 ASP cc_start: 0.8804 (t0) cc_final: 0.8518 (t0) REVERT: B 149 MET cc_start: 0.9223 (mpp) cc_final: 0.9018 (mpp) REVERT: C 24 ASP cc_start: 0.8424 (m-30) cc_final: 0.8107 (m-30) REVERT: D 60 ASN cc_start: 0.7872 (t0) cc_final: 0.7042 (t0) REVERT: D 62 GLN cc_start: 0.8821 (mm110) cc_final: 0.8541 (mp-120) REVERT: D 109 ASP cc_start: 0.9032 (t0) cc_final: 0.8747 (t0) REVERT: D 113 SER cc_start: 0.9451 (t) cc_final: 0.9079 (p) REVERT: E 24 ASP cc_start: 0.8591 (m-30) cc_final: 0.8149 (p0) REVERT: E 152 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8806 (pp) REVERT: E 294 PHE cc_start: 0.9267 (m-80) cc_final: 0.8904 (m-80) REVERT: F 101 LEU cc_start: 0.9014 (mp) cc_final: 0.8790 (mt) REVERT: F 141 TYR cc_start: 0.7689 (m-80) cc_final: 0.7257 (m-80) REVERT: J 3 GLN cc_start: 0.8784 (mm110) cc_final: 0.8472 (mm-40) REVERT: J 47 LEU cc_start: 0.9144 (mp) cc_final: 0.8895 (mp) REVERT: G 46 GLU cc_start: 0.6840 (mp0) cc_final: 0.6249 (mp0) REVERT: G 59 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8793 (mm) REVERT: G 77 GLN cc_start: 0.8280 (pp30) cc_final: 0.7503 (pp30) REVERT: G 78 PHE cc_start: 0.7969 (p90) cc_final: 0.7429 (p90) outliers start: 7 outliers final: 0 residues processed: 388 average time/residue: 0.2692 time to fit residues: 160.6061 Evaluate side-chains 278 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 111 HIS B 169 ASN C 60 GLN C 191 GLN C 196 HIS C 250 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 62 GLN D 79 ASN D 125 GLN E 141 HIS E 142 ASN E 158 ASN E 208 HIS E 285 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN K 27 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17712 Z= 0.424 Angle : 0.708 10.823 24030 Z= 0.368 Chirality : 0.045 0.261 2721 Planarity : 0.005 0.045 3063 Dihedral : 7.606 64.143 3067 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.34 % Allowed : 11.34 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2139 helix: 2.26 (0.26), residues: 381 sheet: 0.86 (0.23), residues: 522 loop : -0.68 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 153 HIS 0.009 0.002 HIS E 184 PHE 0.025 0.002 PHE C 147 TYR 0.029 0.002 TYR L 49 ARG 0.008 0.001 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 267 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8452 (mp10) cc_final: 0.8196 (mp10) REVERT: L 15 VAL cc_start: 0.8961 (m) cc_final: 0.8730 (t) REVERT: L 32 TRP cc_start: 0.8715 (m-10) cc_final: 0.8180 (m-10) REVERT: L 82 ASP cc_start: 0.8769 (m-30) cc_final: 0.8492 (m-30) REVERT: H 39 GLN cc_start: 0.9284 (tt0) cc_final: 0.8822 (tt0) REVERT: H 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8734 (t0) REVERT: H 72 ASP cc_start: 0.8987 (p0) cc_final: 0.8771 (p0) REVERT: H 105 GLN cc_start: 0.9051 (mm110) cc_final: 0.8587 (pp30) REVERT: A 14 CYS cc_start: 0.8738 (m) cc_final: 0.8148 (m) REVERT: A 53 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 54 LEU cc_start: 0.8960 (tp) cc_final: 0.8733 (tt) REVERT: A 105 TYR cc_start: 0.8644 (t80) cc_final: 0.8365 (t80) REVERT: A 225 ASP cc_start: 0.8266 (t70) cc_final: 0.7940 (t0) REVERT: B 59 MET cc_start: 0.8950 (tpp) cc_final: 0.8724 (tpp) REVERT: B 112 ASP cc_start: 0.8766 (t0) cc_final: 0.8537 (t0) REVERT: C 24 ASP cc_start: 0.8386 (m-30) cc_final: 0.8069 (m-30) REVERT: D 77 MET cc_start: 0.8615 (mtt) cc_final: 0.8210 (mtt) REVERT: D 109 ASP cc_start: 0.9054 (t0) cc_final: 0.8700 (t0) REVERT: D 112 ASP cc_start: 0.9118 (m-30) cc_final: 0.8718 (t0) REVERT: D 113 SER cc_start: 0.9591 (t) cc_final: 0.9244 (p) REVERT: E 24 ASP cc_start: 0.8601 (m-30) cc_final: 0.8206 (p0) REVERT: E 98 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: F 101 LEU cc_start: 0.8950 (mp) cc_final: 0.8583 (mt) REVERT: F 141 TYR cc_start: 0.7943 (m-80) cc_final: 0.7373 (m-80) REVERT: J 47 LEU cc_start: 0.9287 (mp) cc_final: 0.8919 (mp) REVERT: G 46 GLU cc_start: 0.7262 (mp0) cc_final: 0.6502 (mp0) REVERT: G 77 GLN cc_start: 0.8195 (pp30) cc_final: 0.7703 (pp30) outliers start: 44 outliers final: 20 residues processed: 297 average time/residue: 0.2651 time to fit residues: 125.0132 Evaluate side-chains 259 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 158 ASN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 5 GLN K 38 GLN K 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17712 Z= 0.170 Angle : 0.579 10.429 24030 Z= 0.294 Chirality : 0.043 0.248 2721 Planarity : 0.004 0.039 3063 Dihedral : 6.076 59.248 3063 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.60 % Allowed : 13.42 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.61 (0.18), residues: 2139 helix: 2.52 (0.27), residues: 381 sheet: 1.09 (0.23), residues: 516 loop : -0.60 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 32 HIS 0.003 0.001 HIS F 26 PHE 0.020 0.001 PHE I 78 TYR 0.020 0.001 TYR C 168 ARG 0.005 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8359 (mp10) cc_final: 0.8094 (mp10) REVERT: L 15 VAL cc_start: 0.9003 (m) cc_final: 0.8768 (t) REVERT: L 82 ASP cc_start: 0.8724 (m-30) cc_final: 0.8438 (m-30) REVERT: H 39 GLN cc_start: 0.9290 (tt0) cc_final: 0.8522 (tm-30) REVERT: H 60 ASN cc_start: 0.9243 (t0) cc_final: 0.8722 (t0) REVERT: H 72 ASP cc_start: 0.8963 (p0) cc_final: 0.8756 (p0) REVERT: H 100 ILE cc_start: 0.8872 (tp) cc_final: 0.8643 (mp) REVERT: H 105 GLN cc_start: 0.9035 (mm110) cc_final: 0.8714 (pp30) REVERT: A 14 CYS cc_start: 0.8677 (m) cc_final: 0.7974 (m) REVERT: A 225 ASP cc_start: 0.8244 (t70) cc_final: 0.7906 (t0) REVERT: B 59 MET cc_start: 0.8765 (tpp) cc_final: 0.8544 (tpp) REVERT: B 90 ASP cc_start: 0.8436 (m-30) cc_final: 0.8158 (m-30) REVERT: B 112 ASP cc_start: 0.8691 (t0) cc_final: 0.8450 (t0) REVERT: C 24 ASP cc_start: 0.8428 (m-30) cc_final: 0.8138 (m-30) REVERT: D 17 MET cc_start: 0.8843 (ttp) cc_final: 0.8638 (ppp) REVERT: D 59 MET cc_start: 0.9243 (tpp) cc_final: 0.8663 (tpp) REVERT: D 77 MET cc_start: 0.8563 (mtt) cc_final: 0.8151 (mtt) REVERT: D 106 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8850 (ttm110) REVERT: D 109 ASP cc_start: 0.8989 (t0) cc_final: 0.8491 (t0) REVERT: D 112 ASP cc_start: 0.9072 (m-30) cc_final: 0.8768 (p0) REVERT: D 113 SER cc_start: 0.9550 (t) cc_final: 0.8878 (p) REVERT: E 14 CYS cc_start: 0.7024 (m) cc_final: 0.6731 (t) REVERT: E 24 ASP cc_start: 0.8457 (m-30) cc_final: 0.8257 (p0) REVERT: E 98 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: E 152 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8240 (pt) REVERT: F 17 MET cc_start: 0.7470 (ttp) cc_final: 0.6848 (ttp) REVERT: F 42 GLN cc_start: 0.8623 (tt0) cc_final: 0.8072 (tm-30) REVERT: F 101 LEU cc_start: 0.8902 (mp) cc_final: 0.8496 (mt) REVERT: F 113 SER cc_start: 0.9565 (t) cc_final: 0.9183 (p) REVERT: F 141 TYR cc_start: 0.7817 (m-80) cc_final: 0.7502 (m-80) REVERT: J 36 TYR cc_start: 0.8021 (m-80) cc_final: 0.7796 (m-10) REVERT: J 47 LEU cc_start: 0.9283 (mp) cc_final: 0.8947 (mp) REVERT: G 77 GLN cc_start: 0.8240 (pp30) cc_final: 0.7780 (pp30) REVERT: I 75 LYS cc_start: 0.9303 (mppt) cc_final: 0.9093 (mtmm) REVERT: I 100 PHE cc_start: 0.9029 (m-80) cc_final: 0.8766 (m-80) outliers start: 30 outliers final: 16 residues processed: 300 average time/residue: 0.2643 time to fit residues: 125.9300 Evaluate side-chains 273 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 17712 Z= 0.482 Angle : 0.722 14.994 24030 Z= 0.372 Chirality : 0.045 0.250 2721 Planarity : 0.005 0.048 3063 Dihedral : 5.851 59.885 3063 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 15.39 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2139 helix: 2.23 (0.26), residues: 381 sheet: 0.73 (0.24), residues: 495 loop : -0.78 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 153 HIS 0.009 0.002 HIS C 184 PHE 0.021 0.002 PHE I 78 TYR 0.019 0.002 TYR C 168 ARG 0.005 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8391 (mp10) cc_final: 0.8003 (mp10) REVERT: L 15 VAL cc_start: 0.9035 (m) cc_final: 0.8819 (t) REVERT: L 32 TRP cc_start: 0.8728 (m-10) cc_final: 0.8109 (m-10) REVERT: L 45 ASN cc_start: 0.8977 (t0) cc_final: 0.8745 (t0) REVERT: L 82 ASP cc_start: 0.8685 (m-30) cc_final: 0.8388 (m-30) REVERT: H 33 CYS cc_start: 0.7057 (m) cc_final: 0.6582 (m) REVERT: H 60 ASN cc_start: 0.9264 (t0) cc_final: 0.8689 (t0) REVERT: H 100 LEU cc_start: 0.8770 (mp) cc_final: 0.8385 (mm) REVERT: H 105 GLN cc_start: 0.9028 (mm110) cc_final: 0.8499 (pp30) REVERT: A 14 CYS cc_start: 0.8673 (m) cc_final: 0.7927 (m) REVERT: A 225 ASP cc_start: 0.8274 (t70) cc_final: 0.7909 (t0) REVERT: B 59 MET cc_start: 0.8899 (tpp) cc_final: 0.8650 (tpp) REVERT: B 90 ASP cc_start: 0.8578 (m-30) cc_final: 0.8313 (m-30) REVERT: B 106 ARG cc_start: 0.9524 (mmm-85) cc_final: 0.9231 (tpp80) REVERT: D 17 MET cc_start: 0.9088 (ttp) cc_final: 0.8773 (ppp) REVERT: D 59 MET cc_start: 0.9240 (tpp) cc_final: 0.8945 (tpp) REVERT: D 109 ASP cc_start: 0.9027 (t0) cc_final: 0.8751 (t0) REVERT: D 112 ASP cc_start: 0.9147 (m-30) cc_final: 0.8687 (t0) REVERT: E 14 CYS cc_start: 0.6980 (m) cc_final: 0.6621 (t) REVERT: E 24 ASP cc_start: 0.8527 (m-30) cc_final: 0.8243 (p0) REVERT: E 98 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: F 101 LEU cc_start: 0.9028 (mp) cc_final: 0.8643 (mt) REVERT: F 113 SER cc_start: 0.9616 (t) cc_final: 0.9320 (p) REVERT: F 141 TYR cc_start: 0.8238 (m-80) cc_final: 0.7619 (m-80) REVERT: J 47 LEU cc_start: 0.9322 (mp) cc_final: 0.8818 (mp) REVERT: G 46 GLU cc_start: 0.7450 (mp0) cc_final: 0.7228 (mp0) REVERT: G 77 GLN cc_start: 0.8297 (pp30) cc_final: 0.7888 (pp30) REVERT: G 87 THR cc_start: 0.8972 (t) cc_final: 0.8703 (m) REVERT: G 97 ILE cc_start: 0.9312 (mm) cc_final: 0.9067 (tp) outliers start: 55 outliers final: 35 residues processed: 283 average time/residue: 0.2612 time to fit residues: 117.5975 Evaluate side-chains 252 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 125 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17712 Z= 0.291 Angle : 0.607 11.341 24030 Z= 0.314 Chirality : 0.043 0.242 2721 Planarity : 0.004 0.049 3063 Dihedral : 5.469 58.143 3063 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.40 % Allowed : 16.45 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2139 helix: 2.48 (0.27), residues: 381 sheet: 0.71 (0.24), residues: 516 loop : -0.72 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 32 HIS 0.004 0.001 HIS E 184 PHE 0.018 0.002 PHE I 78 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.000 ARG I 100F *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8342 (mp10) cc_final: 0.7928 (mp10) REVERT: L 15 VAL cc_start: 0.9058 (m) cc_final: 0.8825 (t) REVERT: L 32 TRP cc_start: 0.8693 (m-10) cc_final: 0.8448 (m-10) REVERT: L 45 ASN cc_start: 0.8996 (t0) cc_final: 0.8730 (t0) REVERT: L 70 ASP cc_start: 0.9105 (t0) cc_final: 0.8880 (p0) REVERT: L 82 ASP cc_start: 0.8698 (m-30) cc_final: 0.8418 (m-30) REVERT: H 33 CYS cc_start: 0.7025 (m) cc_final: 0.6106 (m) REVERT: H 56 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.7726 (t) REVERT: H 60 ASN cc_start: 0.9271 (t0) cc_final: 0.8719 (t0) REVERT: H 100 LEU cc_start: 0.8783 (mp) cc_final: 0.8528 (mm) REVERT: A 14 CYS cc_start: 0.8725 (m) cc_final: 0.8030 (m) REVERT: B 59 MET cc_start: 0.8690 (tpp) cc_final: 0.8430 (tpp) REVERT: B 90 ASP cc_start: 0.8538 (m-30) cc_final: 0.8231 (m-30) REVERT: D 59 MET cc_start: 0.9241 (tpp) cc_final: 0.8980 (tpp) REVERT: D 109 ASP cc_start: 0.9007 (t0) cc_final: 0.8719 (t0) REVERT: D 112 ASP cc_start: 0.9098 (m-30) cc_final: 0.8657 (t0) REVERT: E 14 CYS cc_start: 0.7026 (m) cc_final: 0.6783 (t) REVERT: E 24 ASP cc_start: 0.8449 (m-30) cc_final: 0.8241 (p0) REVERT: E 98 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: F 19 ASP cc_start: 0.7637 (m-30) cc_final: 0.7327 (m-30) REVERT: F 101 LEU cc_start: 0.8966 (mp) cc_final: 0.8605 (mt) REVERT: F 113 SER cc_start: 0.9604 (t) cc_final: 0.9303 (p) REVERT: F 141 TYR cc_start: 0.8246 (m-80) cc_final: 0.7665 (m-80) REVERT: J 27 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8741 (tp40) REVERT: J 47 LEU cc_start: 0.9337 (mp) cc_final: 0.8942 (mp) REVERT: G 77 GLN cc_start: 0.8331 (pp30) cc_final: 0.7892 (pp30) REVERT: G 87 THR cc_start: 0.9008 (t) cc_final: 0.8745 (m) REVERT: K 27 GLN cc_start: 0.8431 (mt0) cc_final: 0.8150 (pt0) REVERT: I 100 ARG cc_start: 0.8889 (mmp80) cc_final: 0.8686 (mmp80) outliers start: 45 outliers final: 26 residues processed: 287 average time/residue: 0.2773 time to fit residues: 125.9370 Evaluate side-chains 260 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 17712 Z= 0.487 Angle : 0.725 9.899 24030 Z= 0.372 Chirality : 0.045 0.246 2721 Planarity : 0.005 0.055 3063 Dihedral : 5.700 59.168 3063 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 17.41 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.03 (0.18), residues: 2139 helix: 2.13 (0.26), residues: 381 sheet: 0.28 (0.23), residues: 522 loop : -0.86 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 153 HIS 0.007 0.002 HIS C 184 PHE 0.021 0.002 PHE I 100 TYR 0.013 0.002 TYR A 161 ARG 0.008 0.001 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8304 (mp10) cc_final: 0.7882 (mp10) REVERT: L 32 TRP cc_start: 0.8784 (m-10) cc_final: 0.8382 (m-10) REVERT: L 45 ASN cc_start: 0.9035 (t0) cc_final: 0.8674 (t0) REVERT: L 70 ASP cc_start: 0.9093 (t0) cc_final: 0.8870 (p0) REVERT: L 82 ASP cc_start: 0.8767 (m-30) cc_final: 0.8489 (m-30) REVERT: H 33 CYS cc_start: 0.7007 (m) cc_final: 0.6025 (m) REVERT: H 56 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.7735 (t) REVERT: H 60 ASN cc_start: 0.9288 (t0) cc_final: 0.8702 (t0) REVERT: H 100 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 14 CYS cc_start: 0.8740 (m) cc_final: 0.8062 (m) REVERT: A 107 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 90 ASP cc_start: 0.8627 (m-30) cc_final: 0.8337 (m-30) REVERT: B 106 ARG cc_start: 0.9524 (mmm-85) cc_final: 0.9239 (tpp80) REVERT: D 59 MET cc_start: 0.9362 (tpp) cc_final: 0.9111 (tpp) REVERT: D 77 MET cc_start: 0.8773 (mtt) cc_final: 0.8552 (mtt) REVERT: D 103 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8563 (mm-30) REVERT: D 106 ARG cc_start: 0.9098 (ttm-80) cc_final: 0.8644 (ttm110) REVERT: D 109 ASP cc_start: 0.9041 (t0) cc_final: 0.8819 (t0) REVERT: D 112 ASP cc_start: 0.9175 (m-30) cc_final: 0.8702 (t0) REVERT: D 119 TYR cc_start: 0.9173 (t80) cc_final: 0.8970 (t80) REVERT: E 24 ASP cc_start: 0.8513 (m-30) cc_final: 0.8237 (p0) REVERT: F 19 ASP cc_start: 0.7781 (m-30) cc_final: 0.7464 (m-30) REVERT: F 101 LEU cc_start: 0.9019 (mp) cc_final: 0.8669 (mt) REVERT: F 113 SER cc_start: 0.9643 (t) cc_final: 0.9371 (p) REVERT: F 141 TYR cc_start: 0.8477 (m-80) cc_final: 0.7826 (m-80) REVERT: J 47 LEU cc_start: 0.9317 (mp) cc_final: 0.8825 (mp) REVERT: G 77 GLN cc_start: 0.8439 (pp30) cc_final: 0.8030 (pp30) REVERT: G 87 THR cc_start: 0.8943 (t) cc_final: 0.8674 (m) REVERT: K 27 GLN cc_start: 0.8505 (mt0) cc_final: 0.8228 (pt0) REVERT: I 72 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7881 (p0) REVERT: I 100 ARG cc_start: 0.8854 (mmp80) cc_final: 0.8595 (mmp80) outliers start: 57 outliers final: 41 residues processed: 265 average time/residue: 0.2696 time to fit residues: 113.3201 Evaluate side-chains 255 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain K residue 45 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 72 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 46 ASN D 62 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17712 Z= 0.173 Angle : 0.613 13.165 24030 Z= 0.308 Chirality : 0.044 0.239 2721 Planarity : 0.004 0.044 3063 Dihedral : 5.275 57.743 3063 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.86 % Allowed : 18.64 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2139 helix: 2.54 (0.27), residues: 381 sheet: 0.43 (0.23), residues: 522 loop : -0.67 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 180 HIS 0.006 0.001 HIS F 26 PHE 0.017 0.002 PHE I 78 TYR 0.011 0.001 TYR L 49 ARG 0.006 0.000 ARG H 100F *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8258 (mp10) cc_final: 0.7656 (mp10) REVERT: L 24 ARG cc_start: 0.9429 (ttt90) cc_final: 0.9102 (ttm-80) REVERT: L 27 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8246 (mm-40) REVERT: L 45 ASN cc_start: 0.9014 (t0) cc_final: 0.8684 (t0) REVERT: L 70 ASP cc_start: 0.9076 (t0) cc_final: 0.8864 (p0) REVERT: L 82 ASP cc_start: 0.8718 (m-30) cc_final: 0.8432 (m-30) REVERT: H 33 CYS cc_start: 0.6910 (m) cc_final: 0.5818 (m) REVERT: H 60 ASN cc_start: 0.9259 (t0) cc_final: 0.8679 (t0) REVERT: H 100 ILE cc_start: 0.8974 (tp) cc_final: 0.8734 (mp) REVERT: H 100 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 14 CYS cc_start: 0.8800 (m) cc_final: 0.8151 (m) REVERT: B 90 ASP cc_start: 0.8533 (m-30) cc_final: 0.8215 (m-30) REVERT: B 102 LEU cc_start: 0.9470 (tp) cc_final: 0.9267 (tt) REVERT: B 168 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9545 (pp) REVERT: D 59 MET cc_start: 0.9311 (tpp) cc_final: 0.9087 (tpp) REVERT: D 106 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8577 (ttm-80) REVERT: D 109 ASP cc_start: 0.8933 (t0) cc_final: 0.8726 (t0) REVERT: D 112 ASP cc_start: 0.9094 (m-30) cc_final: 0.8642 (t0) REVERT: E 98 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: F 17 MET cc_start: 0.7984 (ttp) cc_final: 0.7418 (ttp) REVERT: F 19 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: F 42 GLN cc_start: 0.8793 (tt0) cc_final: 0.8429 (tt0) REVERT: F 101 LEU cc_start: 0.8920 (mp) cc_final: 0.8566 (mt) REVERT: F 113 SER cc_start: 0.9599 (t) cc_final: 0.9277 (p) REVERT: F 141 TYR cc_start: 0.8238 (m-80) cc_final: 0.7804 (m-80) REVERT: J 47 LEU cc_start: 0.9249 (mp) cc_final: 0.8849 (mp) REVERT: G 77 GLN cc_start: 0.8456 (pp30) cc_final: 0.8142 (pp30) REVERT: G 87 THR cc_start: 0.8960 (t) cc_final: 0.8718 (m) REVERT: G 105 GLN cc_start: 0.8599 (mt0) cc_final: 0.8330 (mp10) REVERT: K 27 GLN cc_start: 0.8524 (mt0) cc_final: 0.8259 (pt0) REVERT: I 3 GLN cc_start: 0.8135 (mm110) cc_final: 0.7817 (mm-40) outliers start: 35 outliers final: 21 residues processed: 274 average time/residue: 0.2657 time to fit residues: 114.7961 Evaluate side-chains 254 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 17 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17712 Z= 0.240 Angle : 0.621 12.012 24030 Z= 0.311 Chirality : 0.043 0.240 2721 Planarity : 0.004 0.046 3063 Dihedral : 5.138 58.978 3063 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.13 % Allowed : 19.60 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2139 helix: 2.50 (0.27), residues: 381 sheet: 0.62 (0.23), residues: 510 loop : -0.70 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 180 HIS 0.003 0.001 HIS C 184 PHE 0.017 0.002 PHE J 98 TYR 0.019 0.001 TYR D 119 ARG 0.010 0.000 ARG H 100F *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8283 (mp10) cc_final: 0.7676 (mp10) REVERT: L 24 ARG cc_start: 0.9440 (ttt90) cc_final: 0.9118 (ttm-80) REVERT: L 27 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8266 (mm-40) REVERT: L 32 TRP cc_start: 0.8667 (m-10) cc_final: 0.8339 (m-10) REVERT: L 45 ASN cc_start: 0.9021 (t0) cc_final: 0.8676 (t0) REVERT: L 82 ASP cc_start: 0.8701 (m-30) cc_final: 0.8467 (m-30) REVERT: H 33 CYS cc_start: 0.6844 (m) cc_final: 0.5858 (m) REVERT: H 56 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.7756 (t) REVERT: H 60 ASN cc_start: 0.9292 (t0) cc_final: 0.8708 (t0) REVERT: H 100 ILE cc_start: 0.8978 (tp) cc_final: 0.8669 (mp) REVERT: H 100 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 14 CYS cc_start: 0.8748 (m) cc_final: 0.8118 (m) REVERT: B 90 ASP cc_start: 0.8559 (m-30) cc_final: 0.8249 (m-30) REVERT: B 168 LEU cc_start: 0.9809 (OUTLIER) cc_final: 0.9546 (pp) REVERT: D 59 MET cc_start: 0.9345 (tpp) cc_final: 0.9114 (tpp) REVERT: D 97 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: D 106 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8582 (ttm-80) REVERT: D 109 ASP cc_start: 0.8941 (t0) cc_final: 0.8732 (t0) REVERT: D 112 ASP cc_start: 0.9142 (m-30) cc_final: 0.8696 (t0) REVERT: E 98 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: F 17 MET cc_start: 0.8088 (ttp) cc_final: 0.7614 (ttp) REVERT: F 19 ASP cc_start: 0.7699 (m-30) cc_final: 0.7317 (m-30) REVERT: F 101 LEU cc_start: 0.8950 (mp) cc_final: 0.8637 (mt) REVERT: F 141 TYR cc_start: 0.8295 (m-80) cc_final: 0.7755 (m-80) REVERT: F 149 MET cc_start: 0.8714 (ttp) cc_final: 0.8444 (ttt) REVERT: J 47 LEU cc_start: 0.9267 (mp) cc_final: 0.8878 (mp) REVERT: G 77 GLN cc_start: 0.8462 (pp30) cc_final: 0.8130 (pp30) REVERT: G 87 THR cc_start: 0.8951 (t) cc_final: 0.8696 (m) REVERT: K 27 GLN cc_start: 0.8541 (mt0) cc_final: 0.8267 (pt0) REVERT: I 3 GLN cc_start: 0.8132 (mm110) cc_final: 0.7835 (mm-40) outliers start: 40 outliers final: 27 residues processed: 255 average time/residue: 0.2848 time to fit residues: 115.8978 Evaluate side-chains 257 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 225 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17712 Z= 0.220 Angle : 0.622 12.423 24030 Z= 0.310 Chirality : 0.043 0.240 2721 Planarity : 0.004 0.049 3063 Dihedral : 5.114 59.733 3063 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.86 % Allowed : 19.38 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2139 helix: 2.51 (0.27), residues: 381 sheet: 0.63 (0.23), residues: 510 loop : -0.71 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS D 111 PHE 0.024 0.002 PHE H 78 TYR 0.018 0.001 TYR D 119 ARG 0.013 0.000 ARG H 100F *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8250 (mp10) cc_final: 0.7698 (mp10) REVERT: L 27 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8348 (mm-40) REVERT: L 45 ASN cc_start: 0.9022 (t0) cc_final: 0.8671 (t0) REVERT: L 82 ASP cc_start: 0.8665 (m-30) cc_final: 0.8341 (m-30) REVERT: H 33 CYS cc_start: 0.6865 (m) cc_final: 0.5989 (m) REVERT: H 60 ASN cc_start: 0.9280 (t0) cc_final: 0.8679 (t0) REVERT: H 100 ILE cc_start: 0.9058 (tp) cc_final: 0.8783 (mp) REVERT: H 100 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 14 CYS cc_start: 0.8733 (m) cc_final: 0.8138 (m) REVERT: B 168 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9551 (pp) REVERT: D 59 MET cc_start: 0.9334 (tpp) cc_final: 0.9089 (tpp) REVERT: D 97 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7920 (tp30) REVERT: D 106 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8588 (ttm-80) REVERT: D 109 ASP cc_start: 0.8904 (t0) cc_final: 0.8535 (t0) REVERT: D 112 ASP cc_start: 0.9128 (m-30) cc_final: 0.8755 (p0) REVERT: D 113 SER cc_start: 0.9598 (t) cc_final: 0.8893 (p) REVERT: E 98 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: F 17 MET cc_start: 0.8121 (ttp) cc_final: 0.7639 (ttp) REVERT: F 19 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: F 77 MET cc_start: 0.8730 (mmm) cc_final: 0.8506 (mmm) REVERT: F 101 LEU cc_start: 0.8953 (mp) cc_final: 0.8634 (mt) REVERT: F 141 TYR cc_start: 0.8284 (m-80) cc_final: 0.7763 (m-80) REVERT: J 47 LEU cc_start: 0.9240 (mp) cc_final: 0.8816 (mp) REVERT: G 77 GLN cc_start: 0.8470 (pp30) cc_final: 0.8144 (pp30) REVERT: G 87 THR cc_start: 0.8933 (t) cc_final: 0.8677 (m) REVERT: G 97 ILE cc_start: 0.9296 (mm) cc_final: 0.9005 (tp) REVERT: G 105 GLN cc_start: 0.8599 (mt0) cc_final: 0.8336 (mp10) REVERT: K 27 GLN cc_start: 0.8541 (mt0) cc_final: 0.8270 (pt0) REVERT: I 3 GLN cc_start: 0.8119 (mm110) cc_final: 0.7833 (mm-40) outliers start: 35 outliers final: 26 residues processed: 262 average time/residue: 0.2711 time to fit residues: 112.1377 Evaluate side-chains 262 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 33 CYS Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17712 Z= 0.187 Angle : 0.624 13.147 24030 Z= 0.308 Chirality : 0.043 0.238 2721 Planarity : 0.004 0.067 3063 Dihedral : 4.933 59.519 3063 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.81 % Allowed : 19.65 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2139 helix: 2.50 (0.27), residues: 381 sheet: 0.70 (0.23), residues: 510 loop : -0.68 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS D 111 PHE 0.018 0.001 PHE L 98 TYR 0.018 0.001 TYR D 119 ARG 0.018 0.001 ARG E 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8247 (mp10) cc_final: 0.7689 (mp10) REVERT: L 27 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8320 (mm-40) REVERT: L 45 ASN cc_start: 0.9031 (t0) cc_final: 0.8678 (t0) REVERT: L 82 ASP cc_start: 0.8664 (m-30) cc_final: 0.8457 (m-30) REVERT: H 33 CYS cc_start: 0.6958 (m) cc_final: 0.6038 (m) REVERT: H 60 ASN cc_start: 0.9276 (t0) cc_final: 0.8670 (t0) REVERT: H 100 ILE cc_start: 0.9081 (tp) cc_final: 0.8845 (mp) REVERT: A 14 CYS cc_start: 0.8777 (m) cc_final: 0.8116 (m) REVERT: B 168 LEU cc_start: 0.9808 (tt) cc_final: 0.9551 (pp) REVERT: D 97 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: D 106 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8750 (ttm-80) REVERT: D 109 ASP cc_start: 0.8881 (t0) cc_final: 0.8468 (t0) REVERT: D 112 ASP cc_start: 0.9088 (m-30) cc_final: 0.8743 (p0) REVERT: D 113 SER cc_start: 0.9583 (t) cc_final: 0.8869 (p) REVERT: E 98 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: F 17 MET cc_start: 0.8110 (ttp) cc_final: 0.7566 (ttp) REVERT: F 19 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: F 101 LEU cc_start: 0.8934 (mp) cc_final: 0.8639 (mt) REVERT: F 141 TYR cc_start: 0.8232 (m-80) cc_final: 0.7697 (m-80) REVERT: J 47 LEU cc_start: 0.9166 (mp) cc_final: 0.8860 (mp) REVERT: G 3 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8452 (mm-40) REVERT: G 77 GLN cc_start: 0.8525 (pp30) cc_final: 0.8210 (pp30) REVERT: G 87 THR cc_start: 0.8917 (t) cc_final: 0.8657 (m) REVERT: G 105 GLN cc_start: 0.8600 (mt0) cc_final: 0.8335 (mp10) REVERT: K 27 GLN cc_start: 0.8534 (mt0) cc_final: 0.8264 (pt0) REVERT: I 3 GLN cc_start: 0.8106 (mm110) cc_final: 0.7803 (mm-40) outliers start: 34 outliers final: 26 residues processed: 265 average time/residue: 0.2606 time to fit residues: 109.7209 Evaluate side-chains 266 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain I residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN E 282 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.048540 restraints weight = 60933.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050655 restraints weight = 30301.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052108 restraints weight = 19656.786| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17712 Z= 0.175 Angle : 0.621 13.270 24030 Z= 0.308 Chirality : 0.043 0.238 2721 Planarity : 0.004 0.060 3063 Dihedral : 4.916 59.907 3063 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.60 % Allowed : 19.60 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.39 (0.18), residues: 2139 helix: 2.51 (0.27), residues: 381 sheet: 0.73 (0.23), residues: 510 loop : -0.68 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 32 HIS 0.003 0.001 HIS D 111 PHE 0.024 0.001 PHE H 78 TYR 0.016 0.001 TYR F 94 ARG 0.013 0.000 ARG E 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3390.38 seconds wall clock time: 63 minutes 35.40 seconds (3815.40 seconds total)