Starting phenix.real_space_refine on Tue Apr 9 22:16:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiw_36332/04_2024/8jiw_36332_updated.pdb" } resolution = 2.88 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= -0.004 sd= 0.119 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: 8 Type Number sf(0) Gaussians K 16 8.98 5 Zn 1 6.06 5 P 1571 5.49 5 Mg 70 5.21 5 S 163 5.16 5 C 37189 2.51 5 N 12655 2.21 5 O 17090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 60": "OE1" <-> "OE2" Residue "BA TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 122": "OE1" <-> "OE2" Residue "BA GLU 140": "OE1" <-> "OE2" Residue "BA TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ASP 78": "OD1" <-> "OD2" Residue "BB ASP 108": "OD1" <-> "OD2" Residue "BB GLU 198": "OE1" <-> "OE2" Residue "BC GLU 84": "OE1" <-> "OE2" Residue "BC GLU 93": "OE1" <-> "OE2" Residue "BC TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 256": "OE1" <-> "OE2" Residue "BE GLU 97": "OE1" <-> "OE2" Residue "BE GLU 165": "OE1" <-> "OE2" Residue "BG GLU 35": "OE1" <-> "OE2" Residue "BG GLU 43": "OE1" <-> "OE2" Residue "BG GLU 93": "OE1" <-> "OE2" Residue "BG GLU 120": "OE1" <-> "OE2" Residue "BG PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG GLU 212": "OE1" <-> "OE2" Residue "BH GLU 15": "OE1" <-> "OE2" Residue "BH GLU 18": "OE1" <-> "OE2" Residue "BH GLU 20": "OE1" <-> "OE2" Residue "BH PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH ASP 156": "OD1" <-> "OD2" Residue "BH GLU 168": "OE1" <-> "OE2" Residue "BI GLU 70": "OE1" <-> "OE2" Residue "BJ GLU 43": "OE1" <-> "OE2" Residue "BJ TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ GLU 66": "OE1" <-> "OE2" Residue "BJ GLU 153": "OE1" <-> "OE2" Residue "BL GLU 32": "OE1" <-> "OE2" Residue "BO GLU 25": "OE1" <-> "OE2" Residue "BO ASP 65": "OD1" <-> "OD2" Residue "BO GLU 130": "OE1" <-> "OE2" Residue "BR PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV GLU 4": "OE1" <-> "OE2" Residue "BV ASP 28": "OD1" <-> "OD2" Residue "BV ASP 40": "OD1" <-> "OD2" Residue "BV ASP 69": "OD1" <-> "OD2" Residue "BW GLU 18": "OE1" <-> "OE2" Residue "BW GLU 49": "OE1" <-> "OE2" Residue "BW GLU 87": "OE1" <-> "OE2" Residue "BX GLU 35": "OE1" <-> "OE2" Residue "BX GLU 52": "OE1" <-> "OE2" Residue "BX ASP 97": "OD1" <-> "OD2" Residue "BX GLU 98": "OE1" <-> "OE2" Residue "BY GLU 92": "OE1" <-> "OE2" Residue "BY GLU 115": "OE1" <-> "OE2" Residue "Be ASP 25": "OD1" <-> "OD2" Residue "BD PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ASP 17": "OD1" <-> "OD2" Residue "BD PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ASP 35": "OD1" <-> "OD2" Residue "BD GLU 169": "OE1" <-> "OE2" Residue "BD ASP 194": "OD1" <-> "OD2" Residue "BF GLU 109": "OE1" <-> "OE2" Residue "BK PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ GLU 108": "OE1" <-> "OE2" Residue "BS PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT GLU 107": "OE1" <-> "OE2" Residue "BT ASP 131": "OD1" <-> "OD2" Residue "Bc GLU 48": "OE1" <-> "OE2" Residue "Bd PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 68755 Number of models: 1 Model: "" Number of chains: 37 Chain: "Ad" Number of atoms: 33567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1571, 33567 Classifications: {'RNA': 1571} Modifications used: {'rna2p': 1, 'rna2p_pur': 139, 'rna2p_pyr': 108, 'rna3p': 35, 'rna3p_pur': 693, 'rna3p_pyr': 585} Link IDs: {'rna2p': 247, 'rna3p': 1323} Chain breaks: 22 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 7 Chain: "BA" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1554 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "BB" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "BC" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1703 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain: "BE" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2088 Classifications: {'peptide': 263} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 12, 'TRANS': 250} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Chain: "BG" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1847 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "BH" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1368 Classifications: {'peptide': 182} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 172} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "BI" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1504 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "BJ" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1504 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain: "BL" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1207 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "BN" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1191 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 9, 'TRANS': 139} Chain: "BO" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 983 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "BR" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "BV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "BW" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1032 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "BX" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1077 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "BY" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "Ba" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "Bb" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "Be" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain breaks: 1 Chain: "Cn" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 237 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "BD" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1623 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "BF" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1416 Classifications: {'peptide': 178} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 171} Chain breaks: 2 Chain: "BK" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 711 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "BP" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "BQ" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "BS" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 822 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 3 Chain: "BT" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1081 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "BU" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 95} Chain: "Bc" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 489 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "Bd" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 403 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Bg" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "BZ" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 521 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain breaks: 1 Chain: "Ad" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Unusual residues: {' K': 14, ' MG': 69} Classifications: {'undetermined': 83} Link IDs: {None: 82} Chain: "BS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Bd" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 65777 SG CYSBd 21 117.607 49.589 76.603 1.00107.42 S ATOM 65801 SG CYSBd 24 115.090 52.138 75.552 1.00107.42 S ATOM 65913 SG CYSBd 39 118.746 52.860 74.888 1.00102.94 S ATOM 65939 SG CYSBd 42 117.544 53.051 78.372 1.00105.24 S Time building chain proxies: 27.20, per 1000 atoms: 0.40 Number of scatterers: 68755 At special positions: 0 Unit cell: (211.86, 240.75, 156.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 16 19.00 S 163 16.00 P 1571 15.00 Mg 70 11.99 O 17090 8.00 N 12655 7.00 C 37189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.74 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNBd 102 " pdb="ZN ZNBd 102 " - pdb=" SG CYSBd 24 " pdb="ZN ZNBd 102 " - pdb=" SG CYSBd 39 " pdb="ZN ZNBd 102 " - pdb=" SG CYSBd 42 " pdb="ZN ZNBd 102 " - pdb=" SG CYSBd 21 " Number of angles added : 6 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 48 sheets defined 29.1% alpha, 15.1% beta 432 base pairs and 792 stacking pairs defined. Time for finding SS restraints: 30.10 Creating SS restraints... Processing helix chain 'BA' and resid 15 through 24 Processing helix chain 'BA' and resid 55 through 69 removed outlier: 3.719A pdb=" N GLUBA 60 " --> pdb=" O GLYBA 56 " (cutoff:3.500A) Processing helix chain 'BA' and resid 75 through 77 No H-bonds generated for 'chain 'BA' and resid 75 through 77' Processing helix chain 'BA' and resid 88 through 92 Processing helix chain 'BA' and resid 135 through 143 removed outlier: 4.023A pdb=" N LEUBA 143 " --> pdb=" O LYSBA 139 " (cutoff:3.500A) Processing helix chain 'BA' and resid 174 through 190 removed outlier: 5.963A pdb=" N PHEBA 179 " --> pdb=" O ILEBA 175 " (cutoff:3.500A) Processing helix chain 'BB' and resid 57 through 60 No H-bonds generated for 'chain 'BB' and resid 57 through 60' Processing helix chain 'BB' and resid 107 through 113 Processing helix chain 'BB' and resid 158 through 175 removed outlier: 4.030A pdb=" N GLNBB 163 " --> pdb=" O SERBB 159 " (cutoff:3.500A) Processing helix chain 'BB' and resid 181 through 186 Processing helix chain 'BB' and resid 193 through 200 Processing helix chain 'BB' and resid 229 through 231 No H-bonds generated for 'chain 'BB' and resid 229 through 231' Processing helix chain 'BC' and resid 54 through 60 Processing helix chain 'BC' and resid 68 through 72 Processing helix chain 'BC' and resid 81 through 86 Processing helix chain 'BC' and resid 135 through 149 Processing helix chain 'BC' and resid 196 through 205 Processing helix chain 'BC' and resid 221 through 236 removed outlier: 4.398A pdb=" N TYRBC 236 " --> pdb=" O LEUBC 232 " (cutoff:3.500A) Processing helix chain 'BC' and resid 253 through 256 No H-bonds generated for 'chain 'BC' and resid 253 through 256' Processing helix chain 'BC' and resid 258 through 261 Processing helix chain 'BE' and resid 22 through 24 No H-bonds generated for 'chain 'BE' and resid 22 through 24' Processing helix chain 'BE' and resid 44 through 48 removed outlier: 4.142A pdb=" N LEUBE 48 " --> pdb=" O ILEBE 45 " (cutoff:3.500A) Processing helix chain 'BE' and resid 61 through 65 Processing helix chain 'BE' and resid 117 through 120 removed outlier: 3.705A pdb=" N LYSBE 120 " --> pdb=" O GLUBE 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 117 through 120' Processing helix chain 'BE' and resid 133 through 135 No H-bonds generated for 'chain 'BE' and resid 133 through 135' Processing helix chain 'BE' and resid 247 through 259 Processing helix chain 'BG' and resid 23 through 28 removed outlier: 4.012A pdb=" N ASNBG 26 " --> pdb=" O LYSBG 23 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEUBG 27 " --> pdb=" O LEUBG 24 " (cutoff:3.500A) Processing helix chain 'BG' and resid 38 through 41 No H-bonds generated for 'chain 'BG' and resid 38 through 41' Processing helix chain 'BG' and resid 141 through 144 No H-bonds generated for 'chain 'BG' and resid 141 through 144' Processing helix chain 'BG' and resid 156 through 158 No H-bonds generated for 'chain 'BG' and resid 156 through 158' Processing helix chain 'BG' and resid 186 through 226 removed outlier: 3.660A pdb=" N LYSBG 207 " --> pdb=" O ILEBG 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARGBG 225 " --> pdb=" O LEUBG 221 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASPBG 226 " --> pdb=" O LYSBG 222 " (cutoff:3.500A) Processing helix chain 'BH' and resid 20 through 30 Processing helix chain 'BH' and resid 36 through 39 No H-bonds generated for 'chain 'BH' and resid 36 through 39' Processing helix chain 'BH' and resid 68 through 75 removed outlier: 3.960A pdb=" N LYSBH 71 " --> pdb=" O ARGBH 68 " (cutoff:3.500A) Proline residue: BH 72 - end of helix Processing helix chain 'BH' and resid 77 through 85 removed outlier: 4.001A pdb=" N VALBH 81 " --> pdb=" O HISBH 77 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARGBH 82 " --> pdb=" O VALBH 78 " (cutoff:3.500A) Processing helix chain 'BH' and resid 127 through 130 No H-bonds generated for 'chain 'BH' and resid 127 through 130' Processing helix chain 'BH' and resid 162 through 164 No H-bonds generated for 'chain 'BH' and resid 162 through 164' Processing helix chain 'BH' and resid 167 through 178 Processing helix chain 'BI' and resid 25 through 27 No H-bonds generated for 'chain 'BI' and resid 25 through 27' Processing helix chain 'BI' and resid 49 through 51 No H-bonds generated for 'chain 'BI' and resid 49 through 51' Processing helix chain 'BI' and resid 89 through 92 No H-bonds generated for 'chain 'BI' and resid 89 through 92' Processing helix chain 'BI' and resid 107 through 117 Processing helix chain 'BI' and resid 149 through 159 removed outlier: 3.716A pdb=" N GLUBI 155 " --> pdb=" O GLNBI 151 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYSBI 156 " --> pdb=" O ARGBI 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARGBI 157 " --> pdb=" O LYSBI 153 " (cutoff:3.500A) Processing helix chain 'BI' and resid 165 through 173 removed outlier: 4.032A pdb=" N GLNBI 170 " --> pdb=" O HISBI 166 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHEBI 171 " --> pdb=" O ILEBI 167 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SERBI 172 " --> pdb=" O GLUBI 168 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLYBI 173 " --> pdb=" O GLUBI 169 " (cutoff:3.500A) Processing helix chain 'BI' and resid 184 through 187 No H-bonds generated for 'chain 'BI' and resid 184 through 187' Processing helix chain 'BI' and resid 197 through 207 removed outlier: 3.770A pdb=" N GLUBI 201 " --> pdb=" O GLYBI 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHEBI 202 " --> pdb=" O LYSBI 198 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 4 through 7 Processing helix chain 'BJ' and resid 23 through 36 Processing helix chain 'BJ' and resid 41 through 63 removed outlier: 3.971A pdb=" N VALBJ 47 " --> pdb=" O GLUBJ 43 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 69 through 84 removed outlier: 5.147A pdb=" N GLUBJ 74 " --> pdb=" O ARGBJ 70 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 95 through 100 removed outlier: 3.839A pdb=" N LEUBJ 99 " --> pdb=" O LEUBJ 95 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALABJ 100 " --> pdb=" O ASPBJ 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 95 through 100' Processing helix chain 'BJ' and resid 103 through 109 removed outlier: 3.775A pdb=" N ARGBJ 109 " --> pdb=" O ASNBJ 105 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 111 through 117 Processing helix chain 'BJ' and resid 124 through 132 Processing helix chain 'BJ' and resid 165 through 167 No H-bonds generated for 'chain 'BJ' and resid 165 through 167' Processing helix chain 'BJ' and resid 173 through 183 Processing helix chain 'BL' and resid 48 through 51 No H-bonds generated for 'chain 'BL' and resid 48 through 51' Processing helix chain 'BN' and resid 30 through 42 Processing helix chain 'BN' and resid 47 through 56 removed outlier: 3.562A pdb=" N VALBN 52 " --> pdb=" O SERBN 48 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEUBN 53 " --> pdb=" O GLNBN 49 " (cutoff:3.500A) Processing helix chain 'BN' and resid 63 through 66 No H-bonds generated for 'chain 'BN' and resid 63 through 66' Processing helix chain 'BN' and resid 71 through 78 Processing helix chain 'BN' and resid 86 through 104 removed outlier: 4.261A pdb=" N ARGBN 104 " --> pdb=" O LYSBN 100 " (cutoff:3.500A) Processing helix chain 'BN' and resid 111 through 131 Processing helix chain 'BN' and resid 143 through 149 removed outlier: 4.475A pdb=" N SERBN 147 " --> pdb=" O SERBN 143 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THRBN 148 " --> pdb=" O THRBN 144 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEUBN 149 " --> pdb=" O THRBN 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 143 through 149' Processing helix chain 'BO' and resid 58 through 60 No H-bonds generated for 'chain 'BO' and resid 58 through 60' Processing helix chain 'BO' and resid 67 through 69 No H-bonds generated for 'chain 'BO' and resid 67 through 69' Processing helix chain 'BO' and resid 71 through 86 removed outlier: 3.737A pdb=" N LYSBO 86 " --> pdb=" O ALABO 82 " (cutoff:3.500A) Processing helix chain 'BO' and resid 110 through 121 removed outlier: 4.189A pdb=" N GLNBO 113 " --> pdb=" O PROBO 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SERBO 114 " --> pdb=" O GLYBO 111 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALABO 115 " --> pdb=" O ALABO 112 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALABO 118 " --> pdb=" O ALABO 115 " (cutoff:3.500A) Processing helix chain 'BR' and resid 7 through 19 Processing helix chain 'BR' and resid 28 through 38 removed outlier: 4.347A pdb=" N GLUBR 37 " --> pdb=" O LYSBR 33 " (cutoff:3.500A) Processing helix chain 'BR' and resid 44 through 61 Processing helix chain 'BR' and resid 100 through 107 Processing helix chain 'BV' and resid 56 through 61 Processing helix chain 'BV' and resid 64 through 78 removed outlier: 3.970A pdb=" N ALABV 77 " --> pdb=" O GLNBV 73 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLUBV 78 " --> pdb=" O LYSBV 74 " (cutoff:3.500A) Processing helix chain 'BW' and resid 6 through 19 Processing helix chain 'BW' and resid 32 through 44 Processing helix chain 'BW' and resid 86 through 93 Processing helix chain 'BW' and resid 113 through 119 Processing helix chain 'BX' and resid 10 through 23 removed outlier: 4.583A pdb=" N TRPBX 22 " --> pdb=" O ARGBX 18 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALABX 23 " --> pdb=" O ASNBX 19 " (cutoff:3.500A) Processing helix chain 'BX' and resid 25 through 31 Processing helix chain 'BX' and resid 34 through 37 Processing helix chain 'BX' and resid 129 through 133 Processing helix chain 'BY' and resid 42 through 53 removed outlier: 3.952A pdb=" N GLUBY 47 " --> pdb=" O ALABY 43 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARGBY 48 " --> pdb=" O ASPBY 44 " (cutoff:3.500A) Processing helix chain 'BY' and resid 85 through 91 removed outlier: 3.617A pdb=" N LYSBY 90 " --> pdb=" O GLUBY 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHEBY 91 " --> pdb=" O ALABY 87 " (cutoff:3.500A) Processing helix chain 'BY' and resid 94 through 99 Processing helix chain 'BY' and resid 110 through 120 Processing helix chain 'BY' and resid 126 through 130 removed outlier: 3.587A pdb=" N THRBY 129 " --> pdb=" O VALBY 126 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 47 through 56 removed outlier: 3.892A pdb=" N ARGBa 51 " --> pdb=" O GLNBa 47 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASPBa 52 " --> pdb=" O ALABa 48 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLUBa 55 " --> pdb=" O ARGBa 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALABa 56 " --> pdb=" O ASPBa 52 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 75 through 80 Processing helix chain 'Ba' and resid 89 through 92 No H-bonds generated for 'chain 'Ba' and resid 89 through 92' Processing helix chain 'Bb' and resid 16 through 18 No H-bonds generated for 'chain 'Bb' and resid 16 through 18' Processing helix chain 'Be' and resid 13 through 17 Processing helix chain 'Be' and resid 33 through 44 Processing helix chain 'Cn' and resid 3 through 24 removed outlier: 3.636A pdb=" N SERCn 24 " --> pdb=" O METCn 20 " (cutoff:3.500A) Processing helix chain 'BD' and resid 10 through 29 Processing helix chain 'BD' and resid 59 through 62 No H-bonds generated for 'chain 'BD' and resid 59 through 62' Processing helix chain 'BD' and resid 67 through 79 removed outlier: 3.786A pdb=" N VALBD 76 " --> pdb=" O LEUBD 72 " (cutoff:3.500A) Processing helix chain 'BD' and resid 101 through 114 Processing helix chain 'BD' and resid 118 through 132 Processing helix chain 'BD' and resid 165 through 168 Processing helix chain 'BF' and resid 29 through 31 No H-bonds generated for 'chain 'BF' and resid 29 through 31' Processing helix chain 'BF' and resid 73 through 75 No H-bonds generated for 'chain 'BF' and resid 73 through 75' Processing helix chain 'BF' and resid 79 through 85 Processing helix chain 'BF' and resid 97 through 115 Processing helix chain 'BF' and resid 119 through 128 Processing helix chain 'BF' and resid 154 through 173 Processing helix chain 'BF' and resid 180 through 190 Processing helix chain 'BF' and resid 199 through 212 Processing helix chain 'BK' and resid 5 through 17 Processing helix chain 'BK' and resid 39 through 52 removed outlier: 4.123A pdb=" N SERBK 51 " --> pdb=" O GLNBK 47 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYSBK 52 " --> pdb=" O SERBK 48 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 80 Processing helix chain 'BP' and resid 38 through 42 Processing helix chain 'BP' and resid 45 through 52 Processing helix chain 'BP' and resid 57 through 69 Processing helix chain 'BP' and resid 93 through 95 No H-bonds generated for 'chain 'BP' and resid 93 through 95' Processing helix chain 'BQ' and resid 40 through 42 No H-bonds generated for 'chain 'BQ' and resid 40 through 42' Processing helix chain 'BQ' and resid 46 through 52 removed outlier: 4.518A pdb=" N LEUBQ 50 " --> pdb=" O METBQ 47 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 54 through 59 Processing helix chain 'BQ' and resid 61 through 64 Processing helix chain 'BQ' and resid 78 through 100 removed outlier: 3.772A pdb=" N ALABQ 90 " --> pdb=" O ARGBQ 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYRBQ 97 " --> pdb=" O LEUBQ 93 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYRBQ 100 " --> pdb=" O TYRBQ 96 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 104 through 116 Processing helix chain 'BS' and resid 26 through 29 No H-bonds generated for 'chain 'BS' and resid 26 through 29' Processing helix chain 'BS' and resid 38 through 45 Processing helix chain 'BS' and resid 61 through 72 removed outlier: 3.540A pdb=" N ASPBS 65 " --> pdb=" O ALABS 61 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGBS 66 " --> pdb=" O GLUBS 62 " (cutoff:3.500A) Processing helix chain 'BS' and resid 75 through 77 No H-bonds generated for 'chain 'BS' and resid 75 through 77' Processing helix chain 'BS' and resid 120 through 123 No H-bonds generated for 'chain 'BS' and resid 120 through 123' Processing helix chain 'BT' and resid 7 through 9 No H-bonds generated for 'chain 'BT' and resid 7 through 9' Processing helix chain 'BT' and resid 12 through 26 Processing helix chain 'BT' and resid 53 through 67 removed outlier: 3.546A pdb=" N TYRBT 66 " --> pdb=" O ALABT 62 " (cutoff:3.500A) Processing helix chain 'BT' and resid 73 through 79 Processing helix chain 'BT' and resid 99 through 110 Processing helix chain 'BT' and resid 126 through 137 Processing helix chain 'BU' and resid 33 through 49 Processing helix chain 'BU' and resid 99 through 106 Processing helix chain 'Bd' and resid 33 through 35 No H-bonds generated for 'chain 'Bd' and resid 33 through 35' Processing helix chain 'Bd' and resid 40 through 45 Processing helix chain 'Bd' and resid 47 through 50 No H-bonds generated for 'chain 'Bd' and resid 47 through 50' Processing helix chain 'BZ' and resid 35 through 45 removed outlier: 3.755A pdb=" N LEUBZ 42 " --> pdb=" O TYRBZ 38 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 53 through 60 Processing helix chain 'BZ' and resid 64 through 77 Processing sheet with id= A, first strand: chain 'BA' and resid 101 through 104 removed outlier: 6.983A pdb=" N LEUBA 125 " --> pdb=" O ILEBA 79 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLNBA 81 " --> pdb=" O LEUBA 125 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILEBA 127 " --> pdb=" O GLNBA 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'BB' and resid 66 through 68 removed outlier: 5.126A pdb=" N ARGBB 87 " --> pdb=" O PHEBB 100 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHEBB 100 " --> pdb=" O ARGBB 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'BB' and resid 120 through 125 removed outlier: 6.403A pdb=" N ARGBB 136 " --> pdb=" O ILEBB 217 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILEBB 217 " --> pdb=" O ARGBB 136 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHEBB 138 " --> pdb=" O VALBB 215 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VALBB 215 " --> pdb=" O PHEBB 138 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'BB' and resid 30 through 33 removed outlier: 3.908A pdb=" N ILEBB 32 " --> pdb=" O GLYBB 44 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLYBB 44 " --> pdb=" O ILEBB 32 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'BC' and resid 126 through 132 removed outlier: 3.872A pdb=" N LYSBC 96 " --> pdb=" O PHEBC 115 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VALBC 117 " --> pdb=" O VALBC 94 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VALBC 94 " --> pdb=" O VALBC 117 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'BC' and resid 172 through 176 removed outlier: 3.540A pdb=" N VALBC 179 " --> pdb=" O CYSBC 176 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARGBC 182 " --> pdb=" O SERBC 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'BE' and resid 70 through 72 Processing sheet with id= H, first strand: chain 'BE' and resid 99 through 103 Processing sheet with id= I, first strand: chain 'BE' and resid 121 through 125 removed outlier: 3.766A pdb=" N ASPBE 171 " --> pdb=" O LYSBE 161 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASPBE 163 " --> pdb=" O ILEBE 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILEBE 169 " --> pdb=" O ASPBE 163 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'BE' and resid 225 through 229 removed outlier: 6.903A pdb=" N VALBE 180 " --> pdb=" O ILEBE 228 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HISBE 209 " --> pdb=" O LYSBE 196 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARGBE 198 " --> pdb=" O THRBE 207 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THRBE 207 " --> pdb=" O ARGBE 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'BG' and resid 13 through 17 removed outlier: 6.567A pdb=" N ILEBG 49 " --> pdb=" O VALBG 116 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'BG' and resid 73 through 77 Processing sheet with id= M, first strand: chain 'BG' and resid 55 through 57 Processing sheet with id= N, first strand: chain 'BH' and resid 49 through 52 Processing sheet with id= O, first strand: chain 'BH' and resid 182 through 186 removed outlier: 6.065A pdb=" N ILEBH 151 " --> pdb=" O VALBH 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLUBH 185 " --> pdb=" O ILEBH 151 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILEBH 153 " --> pdb=" O GLUBH 185 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'BI' and resid 72 through 77 removed outlier: 3.608A pdb=" N ASPBI 80 " --> pdb=" O GLNBI 103 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASPBI 105 " --> pdb=" O LEUBI 78 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEUBI 78 " --> pdb=" O ASPBI 105 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'BI' and resid 42 through 47 removed outlier: 6.613A pdb=" N ARGBI 44 " --> pdb=" O ALABI 57 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALABI 57 " --> pdb=" O ARGBI 44 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VALBI 46 " --> pdb=" O TRPBI 55 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRPBI 55 " --> pdb=" O VALBI 46 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'BJ' and resid 136 through 138 removed outlier: 4.457A pdb=" N ILEBJ 136 " --> pdb=" O VALBJ 143 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'BL' and resid 108 through 111 removed outlier: 3.575A pdb=" N SERBL 79 " --> pdb=" O ILEBL 87 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARGBL 89 " --> pdb=" O CYSBL 77 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N CYSBL 77 " --> pdb=" O ARGBL 89 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLYBL 128 " --> pdb=" O VALBL 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VALBL 141 " --> pdb=" O GLYBL 128 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'BL' and resid 92 through 96 Processing sheet with id= U, first strand: chain 'BO' and resid 41 through 44 removed outlier: 3.537A pdb=" N VALBO 54 " --> pdb=" O VALBO 44 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'BO' and resid 129 through 131 removed outlier: 8.616A pdb=" N GLUBO 130 " --> pdb=" O LEUBO 93 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILEBO 95 " --> pdb=" O GLUBO 130 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VALBO 27 " --> pdb=" O THRBO 91 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUBO 93 " --> pdb=" O VALBO 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLYBO 29 " --> pdb=" O LEUBO 93 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILEBO 95 " --> pdb=" O GLYBO 29 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALABO 31 " --> pdb=" O ILEBO 95 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEUBO 97 " --> pdb=" O ALABO 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'BV' and resid 32 through 37 Processing sheet with id= X, first strand: chain 'BW' and resid 24 through 27 Processing sheet with id= Y, first strand: chain 'BW' and resid 71 through 74 removed outlier: 3.637A pdb=" N LYSBW 124 " --> pdb=" O THRBW 105 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VALBW 103 " --> pdb=" O LEUBW 126 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHEBW 128 " --> pdb=" O TYRBW 101 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYRBW 101 " --> pdb=" O PHEBW 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'BX' and resid 79 through 83 removed outlier: 6.484A pdb=" N GLNBX 72 " --> pdb=" O VALBX 50 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VALBX 50 " --> pdb=" O GLNBX 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALABX 102 " --> pdb=" O VALBX 121 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VALBX 121 " --> pdb=" O ALABX 102 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'BY' and resid 11 through 15 Processing sheet with id= AB, first strand: chain 'BY' and resid 18 through 20 Processing sheet with id= AC, first strand: chain 'Ba' and resid 20 through 22 Processing sheet with id= AD, first strand: chain 'Ba' and resid 36 through 43 Processing sheet with id= AE, first strand: chain 'Bb' and resid 47 through 49 removed outlier: 4.244A pdb=" N PHEBb 34 " --> pdb=" O LYSBb 84 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARGBb 82 " --> pdb=" O ASPBb 36 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'BD' and resid 40 through 45 removed outlier: 3.624A pdb=" N TYRBD 90 " --> pdb=" O ILEBD 51 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'BD' and resid 151 through 158 removed outlier: 3.994A pdb=" N GLYBD 136 " --> pdb=" O METBD 192 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'BF' and resid 134 through 137 Processing sheet with id= AI, first strand: chain 'BK' and resid 21 through 24 Processing sheet with id= AJ, first strand: chain 'BQ' and resid 12 through 17 removed outlier: 3.536A pdb=" N ARGBQ 70 " --> pdb=" O TYRBQ 25 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYSBQ 27 " --> pdb=" O ASPBQ 68 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'BT' and resid 82 through 84 Processing sheet with id= AL, first strand: chain 'BT' and resid 114 through 116 Processing sheet with id= AM, first strand: chain 'BU' and resid 114 through 120 removed outlier: 4.419A pdb=" N LYSBU 90 " --> pdb=" O METBU 60 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'BU' and resid 63 through 70 Processing sheet with id= AO, first strand: chain 'Bc' and resid 37 through 42 removed outlier: 6.403A pdb=" N LYSBc 29 " --> pdb=" O VALBc 10 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VALBc 10 " --> pdb=" O LYSBc 29 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Bg' and resid 43 through 46 Processing sheet with id= AQ, first strand: chain 'Bg' and resid 78 through 83 removed outlier: 6.647A pdb=" N GLYBg 93 " --> pdb=" O GLNBg 79 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VALBg 81 " --> pdb=" O LEUBg 91 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEUBg 91 " --> pdb=" O VALBg 81 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILEBg 83 " --> pdb=" O PHEBg 89 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHEBg 89 " --> pdb=" O ILEBg 83 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLUBg 98 " --> pdb=" O SERBg 94 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASPBg 103 " --> pdb=" O THRBg 109 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THRBg 109 " --> pdb=" O ASPBg 103 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Bg' and resid 151 through 154 Processing sheet with id= AS, first strand: chain 'Bg' and resid 171 through 173 removed outlier: 3.695A pdb=" N ARGBg 172 " --> pdb=" O VALBg 183 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VALBg 183 " --> pdb=" O ARGBg 172 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILEBg 182 " --> pdb=" O TRPBg 194 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASNBg 195 " --> pdb=" O LEUBg 201 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEUBg 201 " --> pdb=" O ASNBg 195 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Bg' and resid 214 through 217 removed outlier: 4.732A pdb=" N ALABg 214 " --> pdb=" O GLYBg 227 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLYBg 227 " --> pdb=" O ALABg 214 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASPBg 237 " --> pdb=" O ARGBg 243 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARGBg 243 " --> pdb=" O ASPBg 237 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Bg' and resid 256 through 258 Processing sheet with id= AV, first strand: chain 'Bg' and resid 314 through 317 removed outlier: 4.063A pdb=" N VALBg 335 " --> pdb=" O GLYBg 12 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLYBg 12 " --> pdb=" O VALBg 335 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYSBg 337 " --> pdb=" O LEUBg 10 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEUBg 10 " --> pdb=" O LYSBg 337 " (cutoff:3.500A) 1075 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1071 hydrogen bonds 1686 hydrogen bond angles 0 basepair planarities 432 basepair parallelities 792 stacking parallelities Total time for adding SS restraints: 49.01 Time building geometry restraints manager: 29.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 424 1.22 - 1.37: 21106 1.37 - 1.52: 37214 1.52 - 1.67: 14222 1.67 - 1.82: 256 Bond restraints: 73222 Sorted by residual: bond pdb=" CG PROBQ 45 " pdb=" CD PROBQ 45 " ideal model delta sigma weight residual 1.512 1.074 0.438 2.70e-02 1.37e+03 2.63e+02 bond pdb=" N PROBQ 45 " pdb=" CD PROBQ 45 " ideal model delta sigma weight residual 1.474 1.577 -0.103 1.40e-02 5.10e+03 5.38e+01 bond pdb=" N1 PSUAd 300 " pdb=" C2 PSUAd 300 " ideal model delta sigma weight residual 1.380 1.494 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" N1 PSUAd 255 " pdb=" C2 PSUAd 255 " ideal model delta sigma weight residual 1.380 1.494 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" N1 PSUAd 636 " pdb=" C2 PSUAd 636 " ideal model delta sigma weight residual 1.380 1.494 -0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 73217 not shown) Histogram of bond angle deviations from ideal: 81.04 - 95.37: 2 95.37 - 109.70: 24659 109.70 - 124.03: 74305 124.03 - 138.36: 7300 138.36 - 152.69: 5 Bond angle restraints: 106271 Sorted by residual: angle pdb=" N PROBQ 45 " pdb=" CD PROBQ 45 " pdb=" CG PROBQ 45 " ideal model delta sigma weight residual 103.80 81.04 22.76 1.20e+00 6.94e-01 3.60e+02 angle pdb=" C1' MA6Ad1792 " pdb=" N9 MA6Ad1792 " pdb=" C4 MA6Ad1792 " ideal model delta sigma weight residual 109.25 152.69 -43.44 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C1' OMGAd 246 " pdb=" N9 OMGAd 246 " pdb=" C4 OMGAd 246 " ideal model delta sigma weight residual 108.29 148.59 -40.30 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C1' OMGAd 246 " pdb=" N9 OMGAd 246 " pdb=" C8 OMGAd 246 " ideal model delta sigma weight residual 142.82 103.05 39.77 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C1' MA6Ad1791 " pdb=" N9 MA6Ad1791 " pdb=" C4 MA6Ad1791 " ideal model delta sigma weight residual 109.25 148.95 -39.70 3.00e+00 1.11e-01 1.75e+02 ... (remaining 106266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 41471 35.93 - 71.86: 4192 71.86 - 107.79: 503 107.79 - 143.72: 21 143.72 - 179.65: 46 Dihedral angle restraints: 46233 sinusoidal: 33589 harmonic: 12644 Sorted by residual: dihedral pdb=" O4' UAd 607 " pdb=" C1' UAd 607 " pdb=" N1 UAd 607 " pdb=" C2 UAd 607 " ideal model delta sinusoidal sigma weight residual 200.00 20.90 179.10 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UAd1294 " pdb=" C1' UAd1294 " pdb=" N1 UAd1294 " pdb=" C2 UAd1294 " ideal model delta sinusoidal sigma weight residual -160.00 14.86 -174.86 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' UAd1305 " pdb=" C1' UAd1305 " pdb=" N1 UAd1305 " pdb=" C2 UAd1305 " ideal model delta sinusoidal sigma weight residual -160.00 11.15 -171.15 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 46230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 11880 0.062 - 0.124: 1065 0.124 - 0.186: 106 0.186 - 0.249: 12 0.249 - 0.311: 1 Chirality restraints: 13064 Sorted by residual: chirality pdb=" C1* PSUAd 451 " pdb=" O4* PSUAd 451 " pdb=" C2* PSUAd 451 " pdb=" C5 PSUAd 451 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA PROBQ 45 " pdb=" N PROBQ 45 " pdb=" C PROBQ 45 " pdb=" CB PROBQ 45 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1* PSUAd 951 " pdb=" O4* PSUAd 951 " pdb=" C2* PSUAd 951 " pdb=" C5 PSUAd 951 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 13061 not shown) Planarity restraints: 7660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMCAd 473 " -0.045 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMCAd 473 " -0.447 2.00e-02 2.50e+03 pdb=" O4' OMCAd 473 " -0.676 2.00e-02 2.50e+03 pdb=" C3' OMCAd 473 " 0.593 2.00e-02 2.50e+03 pdb=" O3' OMCAd 473 " 0.613 2.00e-02 2.50e+03 pdb=" C2' OMCAd 473 " 0.199 2.00e-02 2.50e+03 pdb=" O2' OMCAd 473 " -0.942 2.00e-02 2.50e+03 pdb=" C1' OMCAd 473 " -0.215 2.00e-02 2.50e+03 pdb=" N1 OMCAd 473 " 0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCAd 38 " 0.055 2.00e-02 2.50e+03 5.63e-01 7.14e+03 pdb=" C4' OMCAd 38 " 0.424 2.00e-02 2.50e+03 pdb=" O4' OMCAd 38 " 0.542 2.00e-02 2.50e+03 pdb=" C3' OMCAd 38 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMCAd 38 " -0.597 2.00e-02 2.50e+03 pdb=" C2' OMCAd 38 " -0.189 2.00e-02 2.50e+03 pdb=" O2' OMCAd 38 " 0.949 2.00e-02 2.50e+03 pdb=" C1' OMCAd 38 " 0.233 2.00e-02 2.50e+03 pdb=" N1 OMCAd 38 " -0.825 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGAd 246 " -0.063 2.00e-02 2.50e+03 5.61e-01 7.08e+03 pdb=" C4' OMGAd 246 " -0.416 2.00e-02 2.50e+03 pdb=" O4' OMGAd 246 " -0.524 2.00e-02 2.50e+03 pdb=" C3' OMGAd 246 " 0.594 2.00e-02 2.50e+03 pdb=" O3' OMGAd 246 " 0.590 2.00e-02 2.50e+03 pdb=" C2' OMGAd 246 " 0.185 2.00e-02 2.50e+03 pdb=" O2' OMGAd 246 " -0.951 2.00e-02 2.50e+03 pdb=" C1' OMGAd 246 " -0.241 2.00e-02 2.50e+03 pdb=" N9 OMGAd 246 " 0.826 2.00e-02 2.50e+03 ... (remaining 7657 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.90: 1 1.90 - 2.71: 5557 2.71 - 3.52: 110957 3.52 - 4.33: 245975 4.33 - 5.14: 359982 Nonbonded interactions: 722472 Sorted by model distance: nonbonded pdb="MG MGAd1920 " pdb="MG MGAd1921 " model vdw 1.094 1.300 nonbonded pdb=" OP2 CAd1278 " pdb="MG MGAd1920 " model vdw 1.935 2.170 nonbonded pdb=" OP2 UAd1575 " pdb="MG MGAd1902 " model vdw 1.936 2.170 nonbonded pdb=" OP2 AAd 560 " pdb="MG MGAd1959 " model vdw 1.947 2.170 nonbonded pdb=" OP1 GAd1778 " pdb="MG MGAd1963 " model vdw 1.954 2.170 ... (remaining 722467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 17.160 Check model and map are aligned: 0.780 Set scattering table: 0.520 Process input model: 196.850 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.170 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:10.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 0.438 73222 Z= 0.385 Angle : 0.833 43.443 106271 Z= 0.366 Chirality : 0.037 0.311 13064 Planarity : 0.017 0.597 7660 Dihedral : 23.342 179.650 38077 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer: Outliers : 0.56 % Allowed : 35.04 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.10 % 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: -0.87 (0.13), residues: 4312 helix: 0.37 (0.15), residues: 1290 sheet: -0.57 (0.19), residues: 765 loop : -1.12 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPBT 53 HIS 0.013 0.001 HISBP 85 PHE 0.033 0.001 PHEBR 53 TYR 0.025 0.002 TYRBD 123 ARG 0.020 0.000 ARGBQ 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 672 time to evaluate : 4.064 Fit side-chains TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SERBI 3 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BH 28 PHE cc_start: 0.6095 (m-80) cc_final: 0.5872 (t80) REVERT: BI 78 LEU cc_start: 0.8927 (mp) cc_final: 0.8722 (mp) REVERT: BO 53 LEU cc_start: 0.8173 (mm) cc_final: 0.7873 (tp) REVERT: BO 103 ASN cc_start: 0.7856 (p0) cc_final: 0.7273 (t0) REVERT: BO 132 VAL cc_start: 0.8993 (m) cc_final: 0.8791 (t) REVERT: BX 97 ASP cc_start: 0.7758 (t0) cc_final: 0.7400 (t0) REVERT: BD 185 LEU cc_start: 0.8158 (tp) cc_final: 0.7890 (mt) REVERT: BF 184 LEU cc_start: 0.8909 (mt) cc_final: 0.8603 (tm) REVERT: BP 95 MET cc_start: 0.5061 (pmt) cc_final: 0.4683 (pmm) REVERT: BQ 136 ARG cc_start: 0.6422 (tpp-160) cc_final: 0.6155 (tpp80) REVERT: BS 27 MET cc_start: 0.3971 (tpt) cc_final: 0.3639 (tpp) REVERT: BS 54 LYS cc_start: 0.4297 (mttt) cc_final: 0.3449 (mppt) REVERT: BS 81 ASP cc_start: 0.5465 (t0) cc_final: 0.5106 (t0) REVERT: BT 22 HIS cc_start: 0.6008 (t-90) cc_final: 0.5631 (t-170) REVERT: Bg 14 MET cc_start: 0.3136 (mmt) cc_final: 0.2767 (tpt) outliers start: 21 outliers final: 5 residues processed: 685 average time/residue: 1.5222 time to fit residues: 1356.8781 Evaluate side-chains 625 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 620 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BH residue 12 LYS Chi-restraints excluded: chain BI residue 3 SER Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain BS residue 47 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 493 optimal weight: 20.0000 chunk 442 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 457 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 chunk 340 optimal weight: 0.2980 chunk 530 optimal weight: 5.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 22 GLN ** BG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 25 GLN BH 34 ASN BI 17 GLN ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 26 HIS ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN Be 29 GLN BP 120 HIS BQ 98 GLN BT 77 GLN ** BT 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 282 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 73222 Z= 0.395 Angle : 0.773 18.406 106271 Z= 0.386 Chirality : 0.042 0.462 13064 Planarity : 0.006 0.138 7660 Dihedral : 23.263 179.744 29167 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.93 % Favored : 92.00 % Rotamer: Outliers : 6.89 % Allowed : 32.72 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4312 helix: 0.40 (0.15), residues: 1280 sheet: -0.64 (0.19), residues: 787 loop : -1.21 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPBT 53 HIS 0.010 0.001 HISBP 85 PHE 0.032 0.002 PHEBR 108 TYR 0.025 0.002 TYRBE 58 ARG 0.010 0.001 ARGBd 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 643 time to evaluate : 4.857 Fit side-chains TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 81 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: BC 236 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.6540 (t80) REVERT: BE 19 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: BG 44 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: BH 28 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5892 (t80) REVERT: BI 78 LEU cc_start: 0.8915 (mp) cc_final: 0.8704 (mp) REVERT: BO 53 LEU cc_start: 0.8224 (mm) cc_final: 0.7963 (tp) REVERT: BO 132 VAL cc_start: 0.9053 (m) cc_final: 0.8840 (t) REVERT: BO 143 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8038 (ptmt) REVERT: BV 75 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7900 (tpp80) REVERT: Bb 86 ASP cc_start: 0.5574 (OUTLIER) cc_final: 0.5207 (p0) REVERT: BF 184 LEU cc_start: 0.8936 (mt) cc_final: 0.8654 (tm) REVERT: BK 46 MET cc_start: 0.4171 (tpt) cc_final: 0.3943 (tpt) REVERT: BP 95 MET cc_start: 0.5109 (pmt) cc_final: 0.4712 (pmm) REVERT: BQ 136 ARG cc_start: 0.6442 (tpp-160) cc_final: 0.6183 (tpp80) REVERT: BS 51 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.6013 (p0) REVERT: BS 54 LYS cc_start: 0.4472 (mttt) cc_final: 0.3542 (mppt) REVERT: BT 5 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.2818 (mpp-170) REVERT: BT 55 TYR cc_start: 0.6711 (m-10) cc_final: 0.6504 (m-10) REVERT: BU 63 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7844 (ptmt) REVERT: Bd 28 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5796 (t70) REVERT: Bg 14 MET cc_start: 0.2889 (mmt) cc_final: 0.2535 (tpt) REVERT: Bg 99 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6826 (mm) outliers start: 259 outliers final: 128 residues processed: 809 average time/residue: 1.4232 time to fit residues: 1524.6189 Evaluate side-chains 761 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 621 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 72 ILE Chi-restraints excluded: chain BA residue 118 THR Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 67 GLU Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 86 LEU Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 96 VAL Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 153 THR Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 83 VAL Chi-restraints excluded: chain BC residue 125 VAL Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BE residue 16 SER Chi-restraints excluded: chain BE residue 19 MET Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 198 ARG Chi-restraints excluded: chain BE residue 225 VAL Chi-restraints excluded: chain BE residue 227 THR Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 215 LYS Chi-restraints excluded: chain BH residue 12 LYS Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 28 PHE Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 59 ARG Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BJ residue 163 THR Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 40 VAL Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 6 SER Chi-restraints excluded: chain BN residue 12 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 96 VAL Chi-restraints excluded: chain BO residue 45 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BR residue 104 ASP Chi-restraints excluded: chain BV residue 7 ASP Chi-restraints excluded: chain BV residue 63 ASP Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 118 ARG Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 5 ASN Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 86 ASP Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 81 ASN Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 189 VAL Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BF residue 31 ASN Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 158 VAL Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BQ residue 119 THR Chi-restraints excluded: chain BS residue 51 ASP Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 95 PHE Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 40 THR Chi-restraints excluded: chain BT residue 85 ARG Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 80 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 193 VAL Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 294 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 chunk 361 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 531 optimal weight: 5.9990 chunk 573 optimal weight: 9.9990 chunk 473 optimal weight: 30.0000 chunk 526 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 426 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 34 ASN BI 17 GLN ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 15 GLN ** BR 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN Be 29 GLN BQ 98 GLN BT 77 GLN Bg 282 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 73222 Z= 0.341 Angle : 0.743 17.600 106271 Z= 0.373 Chirality : 0.041 0.451 13064 Planarity : 0.006 0.138 7660 Dihedral : 23.241 179.626 29162 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 7.71 % Allowed : 33.25 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4312 helix: 0.31 (0.15), residues: 1283 sheet: -0.64 (0.18), residues: 783 loop : -1.23 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPBT 53 HIS 0.006 0.001 HISBS 135 PHE 0.025 0.002 PHEBB 38 TYR 0.024 0.002 TYRBE 58 ARG 0.010 0.000 ARGBd 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 653 time to evaluate : 3.970 Fit side-chains TARDY: cannot create tardy model for: "LYSBE 7 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 170 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8048 (mmtp) REVERT: BA 197 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6206 (m-70) REVERT: BB 205 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: BC 81 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: BC 236 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.6913 (t80) REVERT: BE 19 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: BI 78 LEU cc_start: 0.8961 (mp) cc_final: 0.8741 (mp) REVERT: BN 38 THR cc_start: 0.8459 (m) cc_final: 0.8214 (p) REVERT: BO 53 LEU cc_start: 0.8212 (mm) cc_final: 0.7949 (tp) REVERT: BO 132 VAL cc_start: 0.9059 (m) cc_final: 0.8843 (t) REVERT: BO 143 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8066 (ptmt) REVERT: BR 23 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4329 (ttm-80) REVERT: BR 58 MET cc_start: 0.7101 (mmm) cc_final: 0.6768 (mmm) REVERT: BX 118 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7050 (mtp85) REVERT: BY 92 GLU cc_start: 0.7167 (mp0) cc_final: 0.6858 (mp0) REVERT: Be 25 ASP cc_start: 0.7793 (t0) cc_final: 0.7569 (t0) REVERT: Be 55 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.6010 (ttm170) REVERT: Cn 4 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7790 (ttpt) REVERT: BD 185 LEU cc_start: 0.8243 (tp) cc_final: 0.7941 (mt) REVERT: BF 184 LEU cc_start: 0.8902 (mt) cc_final: 0.8620 (tm) REVERT: BK 46 MET cc_start: 0.4219 (tpt) cc_final: 0.3930 (tpt) REVERT: BK 47 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7095 (tm-30) REVERT: BP 39 LEU cc_start: 0.2470 (OUTLIER) cc_final: 0.2233 (pt) REVERT: BP 95 MET cc_start: 0.5090 (pmt) cc_final: 0.4573 (pmt) REVERT: BQ 97 TYR cc_start: 0.5784 (m-10) cc_final: 0.5473 (m-10) REVERT: BQ 136 ARG cc_start: 0.6461 (tpp-160) cc_final: 0.6212 (tpp80) REVERT: BS 54 LYS cc_start: 0.4414 (mttt) cc_final: 0.3505 (mppt) REVERT: BS 64 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.5280 (tpt) REVERT: BT 5 ARG cc_start: 0.4053 (OUTLIER) cc_final: 0.2750 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6397 (t-90) cc_final: 0.5954 (t-170) REVERT: BT 55 TYR cc_start: 0.6758 (m-10) cc_final: 0.6503 (m-10) REVERT: BT 116 VAL cc_start: 0.3868 (OUTLIER) cc_final: 0.3666 (m) REVERT: BU 63 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7878 (ptmt) REVERT: Bd 28 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5524 (t70) REVERT: Bg 14 MET cc_start: 0.2893 (mmt) cc_final: 0.2579 (tpt) REVERT: Bg 99 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6835 (mm) REVERT: BZ 41 LEU cc_start: 0.2789 (OUTLIER) cc_final: 0.2100 (pp) outliers start: 290 outliers final: 147 residues processed: 847 average time/residue: 1.4169 time to fit residues: 1587.7499 Evaluate side-chains 785 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 620 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 72 ILE Chi-restraints excluded: chain BA residue 118 THR Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 170 LYS Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 197 HIS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 86 LEU Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 96 VAL Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 83 VAL Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 164 GLN Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BE residue 7 LYS Chi-restraints excluded: chain BE residue 16 SER Chi-restraints excluded: chain BE residue 19 MET Chi-restraints excluded: chain BE residue 57 THR Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 225 VAL Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 45 TYR Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BH residue 129 ASP Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BI residue 196 GLU Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 59 ARG Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BJ residue 163 THR Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 40 VAL Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BO residue 45 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 55 THR Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BR residue 104 ASP Chi-restraints excluded: chain BV residue 7 ASP Chi-restraints excluded: chain BV residue 63 ASP Chi-restraints excluded: chain BV residue 79 ILE Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 118 ARG Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 11 ASN Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 81 PHE Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Be residue 55 ARG Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 81 ASN Chi-restraints excluded: chain BD residue 118 VAL Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BF residue 31 ASN Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 158 VAL Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 43 ILE Chi-restraints excluded: chain BP residue 39 LEU Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 62 SER Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BQ residue 119 THR Chi-restraints excluded: chain BS residue 64 MET Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 40 THR Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BT residue 116 VAL Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 80 THR Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 193 VAL Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 41 LEU Chi-restraints excluded: chain BZ residue 74 LEU Chi-restraints excluded: chain BZ residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 524 optimal weight: 9.9990 chunk 399 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 533 optimal weight: 30.0000 chunk 564 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 505 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 197 ASN ** BG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 26 HIS ** BR 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN BQ 98 GLN BT 77 GLN ** Bd 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 73222 Z= 0.377 Angle : 0.765 17.673 106271 Z= 0.384 Chirality : 0.042 0.461 13064 Planarity : 0.006 0.140 7660 Dihedral : 23.229 179.913 29158 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.84 % Rotamer: Outliers : 8.73 % Allowed : 33.23 % Favored : 58.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4312 helix: 0.24 (0.15), residues: 1285 sheet: -0.63 (0.19), residues: 779 loop : -1.27 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPBT 34 HIS 0.006 0.001 HISBW 113 PHE 0.042 0.002 PHEBb 81 TYR 0.029 0.002 TYRBE 58 ARG 0.013 0.001 ARGBd 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 653 time to evaluate : 3.979 Fit side-chains TARDY: cannot create tardy model for: "LYSBE 7 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 170 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8025 (mmtp) REVERT: BB 89 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7156 (mm-30) REVERT: BB 205 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: BC 81 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: BC 236 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.6829 (t80) REVERT: BC 255 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8387 (tm130) REVERT: BE 21 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7502 (p0) REVERT: BE 198 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8209 (mtp180) REVERT: BG 65 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7522 (tp-100) REVERT: BH 28 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5941 (t80) REVERT: BH 70 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6529 (ptp-170) REVERT: BI 7 MET cc_start: 0.7307 (tpt) cc_final: 0.6795 (tpt) REVERT: BI 10 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7319 (mtm180) REVERT: BI 41 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7815 (ptmt) REVERT: BI 78 LEU cc_start: 0.8989 (mp) cc_final: 0.8753 (mp) REVERT: BN 38 THR cc_start: 0.8507 (m) cc_final: 0.8271 (p) REVERT: BO 53 LEU cc_start: 0.8196 (mm) cc_final: 0.7930 (tp) REVERT: BO 132 VAL cc_start: 0.9059 (m) cc_final: 0.8841 (t) REVERT: BO 143 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8081 (ptmt) REVERT: BR 23 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4197 (ttm-80) REVERT: BR 58 MET cc_start: 0.7118 (mmm) cc_final: 0.6768 (mmm) REVERT: BR 119 ARG cc_start: 0.6827 (mmp80) cc_final: 0.4959 (tmm160) REVERT: BY 37 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7758 (ptm160) REVERT: Bb 86 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5414 (p0) REVERT: Be 25 ASP cc_start: 0.7856 (t0) cc_final: 0.7589 (t0) REVERT: BD 192 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6933 (ttm) REVERT: BF 184 LEU cc_start: 0.8894 (mt) cc_final: 0.8616 (tm) REVERT: BK 46 MET cc_start: 0.3974 (tpt) cc_final: 0.3680 (tpt) REVERT: BP 39 LEU cc_start: 0.2498 (OUTLIER) cc_final: 0.2193 (pt) REVERT: BP 95 MET cc_start: 0.5073 (pmt) cc_final: 0.4821 (pmm) REVERT: BQ 136 ARG cc_start: 0.6420 (tpp-160) cc_final: 0.6169 (tpp80) REVERT: BS 54 LYS cc_start: 0.4519 (mttt) cc_final: 0.3624 (mppt) REVERT: BS 64 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.5225 (tpt) REVERT: BT 5 ARG cc_start: 0.4133 (OUTLIER) cc_final: 0.2828 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6187 (t-90) cc_final: 0.5775 (t-170) REVERT: BT 55 TYR cc_start: 0.6903 (m-10) cc_final: 0.6620 (m-10) REVERT: BT 77 GLN cc_start: 0.7615 (tt0) cc_final: 0.7288 (tp-100) REVERT: BU 23 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.4841 (mtm180) REVERT: BU 63 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7821 (ptmt) REVERT: Bc 32 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.5854 (p0) REVERT: Bd 28 HIS cc_start: 0.5946 (OUTLIER) cc_final: 0.5581 (t70) REVERT: Bg 99 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6771 (mm) REVERT: Bg 141 ILE cc_start: 0.3820 (OUTLIER) cc_final: 0.3572 (mp) REVERT: BZ 41 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.1836 (pp) REVERT: BZ 45 VAL cc_start: 0.0907 (OUTLIER) cc_final: 0.0631 (p) REVERT: BZ 73 ASP cc_start: 0.6007 (OUTLIER) cc_final: 0.5647 (p0) outliers start: 328 outliers final: 195 residues processed: 880 average time/residue: 1.3918 time to fit residues: 1630.4642 Evaluate side-chains 842 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 618 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 72 ILE Chi-restraints excluded: chain BA residue 77 ASP Chi-restraints excluded: chain BA residue 118 THR Chi-restraints excluded: chain BA residue 119 SER Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 170 LYS Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 67 GLU Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 96 VAL Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 126 ASP Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 130 THR Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 153 THR Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 58 LEU Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 83 VAL Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 125 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 164 GLN Chi-restraints excluded: chain BC residue 180 THR Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 247 THR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 7 LYS Chi-restraints excluded: chain BE residue 16 SER Chi-restraints excluded: chain BE residue 21 ASP Chi-restraints excluded: chain BE residue 57 THR Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 198 ARG Chi-restraints excluded: chain BE residue 225 VAL Chi-restraints excluded: chain BE residue 227 THR Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 247 THR Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 65 GLN Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 217 LEU Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 23 VAL Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 28 PHE Chi-restraints excluded: chain BH residue 45 TYR Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 70 ARG Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BH residue 129 ASP Chi-restraints excluded: chain BH residue 146 ASP Chi-restraints excluded: chain BI residue 10 ARG Chi-restraints excluded: chain BI residue 41 LYS Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 99 ASN Chi-restraints excluded: chain BI residue 121 ILE Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 59 ARG Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BJ residue 163 THR Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 40 VAL Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 6 SER Chi-restraints excluded: chain BN residue 12 SER Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 63 VAL Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BN residue 96 VAL Chi-restraints excluded: chain BO residue 45 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 55 THR Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BR residue 104 ASP Chi-restraints excluded: chain BV residue 7 ASP Chi-restraints excluded: chain BV residue 18 SER Chi-restraints excluded: chain BV residue 63 ASP Chi-restraints excluded: chain BV residue 79 ILE Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 37 ARG Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 11 ASN Chi-restraints excluded: chain Bb residue 36 ASP Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 80 SER Chi-restraints excluded: chain Bb residue 86 ASP Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Be residue 48 VAL Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 81 ASN Chi-restraints excluded: chain BD residue 118 VAL Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BF residue 31 ASN Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 158 VAL Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 32 HIS Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 43 ILE Chi-restraints excluded: chain BK residue 51 SER Chi-restraints excluded: chain BP residue 39 LEU Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 62 SER Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BQ residue 117 ASP Chi-restraints excluded: chain BQ residue 119 THR Chi-restraints excluded: chain BS residue 64 MET Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BS residue 85 ASN Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 40 THR Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 85 ARG Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BU residue 23 ARG Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 80 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 72 THR Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 193 VAL Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 28 ASN Chi-restraints excluded: chain BZ residue 41 LEU Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 66 LEU Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 74 LEU Chi-restraints excluded: chain BZ residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 470 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 420 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 481 optimal weight: 20.0000 chunk 390 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 288 optimal weight: 0.0170 chunk 506 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 103 GLN BG 121 ASN ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BR 15 GLN ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 21 ASN ** BW 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN Be 29 GLN BQ 98 GLN BS 120 HIS ** Bd 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 282 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 73222 Z= 0.302 Angle : 0.737 17.622 106271 Z= 0.371 Chirality : 0.040 0.444 13064 Planarity : 0.006 0.135 7660 Dihedral : 23.213 179.991 29158 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 8.19 % Allowed : 34.50 % Favored : 57.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4312 helix: 0.28 (0.15), residues: 1291 sheet: -0.60 (0.19), residues: 779 loop : -1.25 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPBT 53 HIS 0.010 0.001 HISBS 120 PHE 0.032 0.002 PHEBK 49 TYR 0.035 0.002 TYRBD 123 ARG 0.007 0.000 ARGBT 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 651 time to evaluate : 4.052 Fit side-chains TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 170 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8087 (mmtp) REVERT: BA 200 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.5124 (mt-10) REVERT: BB 205 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: BC 81 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: BC 236 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.6702 (t80) REVERT: BC 255 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8389 (tm130) REVERT: BE 21 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7428 (p0) REVERT: BE 198 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8213 (mtp180) REVERT: BG 44 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: BG 65 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7487 (tp-100) REVERT: BG 134 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5368 (ttm) REVERT: BH 28 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5930 (t80) REVERT: BI 7 MET cc_start: 0.7381 (tpt) cc_final: 0.6884 (tpt) REVERT: BI 10 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7526 (mtm180) REVERT: BI 41 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7883 (ptmt) REVERT: BI 78 LEU cc_start: 0.8976 (mp) cc_final: 0.8718 (mp) REVERT: BN 38 THR cc_start: 0.8381 (m) cc_final: 0.8134 (p) REVERT: BO 53 LEU cc_start: 0.8166 (mm) cc_final: 0.7898 (tp) REVERT: BO 143 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8027 (ptmt) REVERT: BO 151 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7871 (mp) REVERT: BR 23 ARG cc_start: 0.5228 (OUTLIER) cc_final: 0.4252 (ttm-80) REVERT: BR 58 MET cc_start: 0.7246 (mmm) cc_final: 0.6872 (mmm) REVERT: BY 37 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7719 (ptm160) REVERT: Bb 83 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7426 (ttm-80) REVERT: Be 25 ASP cc_start: 0.7873 (t0) cc_final: 0.7604 (t0) REVERT: BD 160 MET cc_start: 0.7575 (tpp) cc_final: 0.7275 (tpt) REVERT: BF 184 LEU cc_start: 0.8897 (mt) cc_final: 0.8613 (tm) REVERT: BK 46 MET cc_start: 0.4027 (tpt) cc_final: 0.3715 (tpt) REVERT: BP 56 LYS cc_start: 0.2190 (OUTLIER) cc_final: 0.0937 (pttt) REVERT: BP 95 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4481 (pmt) REVERT: BS 54 LYS cc_start: 0.4361 (mttt) cc_final: 0.3483 (mppt) REVERT: BS 64 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5025 (tpt) REVERT: BT 5 ARG cc_start: 0.4105 (OUTLIER) cc_final: 0.2803 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6215 (t-90) cc_final: 0.5828 (t-170) REVERT: BT 55 TYR cc_start: 0.6972 (m-10) cc_final: 0.6704 (m-10) REVERT: BU 63 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7840 (ptmt) REVERT: Bc 32 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6041 (p0) REVERT: Bd 28 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5553 (t70) REVERT: Bg 99 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6824 (mm) REVERT: Bg 141 ILE cc_start: 0.3807 (OUTLIER) cc_final: 0.3561 (mp) REVERT: BZ 73 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5628 (p0) outliers start: 308 outliers final: 200 residues processed: 863 average time/residue: 1.4281 time to fit residues: 1640.7169 Evaluate side-chains 851 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 622 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 72 ILE Chi-restraints excluded: chain BA residue 77 ASP Chi-restraints excluded: chain BA residue 118 THR Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 170 LYS Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 200 GLU Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 96 VAL Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 126 ASP Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 130 THR Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 58 LEU Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 83 VAL Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 125 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 164 GLN Chi-restraints excluded: chain BC residue 180 THR Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 247 THR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 16 SER Chi-restraints excluded: chain BE residue 21 ASP Chi-restraints excluded: chain BE residue 32 SER Chi-restraints excluded: chain BE residue 57 THR Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 81 THR Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 198 ARG Chi-restraints excluded: chain BE residue 225 VAL Chi-restraints excluded: chain BE residue 227 THR Chi-restraints excluded: chain BE residue 247 THR Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 65 GLN Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 121 ASN Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 134 MET Chi-restraints excluded: chain BG residue 217 LEU Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 28 PHE Chi-restraints excluded: chain BH residue 45 TYR Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BH residue 129 ASP Chi-restraints excluded: chain BH residue 146 ASP Chi-restraints excluded: chain BI residue 10 ARG Chi-restraints excluded: chain BI residue 38 SER Chi-restraints excluded: chain BI residue 41 LYS Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 121 ILE Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BI residue 196 GLU Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 59 ARG Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BJ residue 163 THR Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 40 VAL Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 12 SER Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 66 VAL Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BN residue 96 VAL Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 116 LEU Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BO residue 151 LEU Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 55 THR Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BR residue 104 ASP Chi-restraints excluded: chain BV residue 7 ASP Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BV residue 18 SER Chi-restraints excluded: chain BV residue 63 ASP Chi-restraints excluded: chain BV residue 79 ILE Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 11 THR Chi-restraints excluded: chain BY residue 37 ARG Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 28 LYS Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 83 ARG Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Be residue 48 VAL Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 62 LEU Chi-restraints excluded: chain BD residue 81 ASN Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 31 ASN Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 158 VAL Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 32 HIS Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 43 ILE Chi-restraints excluded: chain BK residue 51 SER Chi-restraints excluded: chain BP residue 56 LYS Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BP residue 95 MET Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 62 SER Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BS residue 64 MET Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 40 THR Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 80 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain BU residue 101 VAL Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bc residue 60 GLU Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 72 THR Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 193 VAL Chi-restraints excluded: chain Bg residue 197 THR Chi-restraints excluded: chain Bg residue 208 HIS Chi-restraints excluded: chain Bg residue 266 CYS Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 28 ASN Chi-restraints excluded: chain BZ residue 66 LEU Chi-restraints excluded: chain BZ residue 71 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 74 LEU Chi-restraints excluded: chain BZ residue 76 GLU Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 189 optimal weight: 0.7980 chunk 508 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 chunk 565 optimal weight: 0.0370 chunk 469 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 296 optimal weight: 8.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 121 ASN ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 26 HIS BR 42 GLN ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 94 ASN Bb 67 GLN BQ 98 GLN BS 120 HIS BT 77 GLN BU 66 ASN ** Bd 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 73222 Z= 0.162 Angle : 0.690 18.038 106271 Z= 0.349 Chirality : 0.036 0.387 13064 Planarity : 0.005 0.125 7660 Dihedral : 23.127 179.808 29158 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 6.09 % Allowed : 36.58 % Favored : 57.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4312 helix: 0.44 (0.15), residues: 1289 sheet: -0.52 (0.19), residues: 783 loop : -1.16 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPBT 53 HIS 0.011 0.001 HISBS 120 PHE 0.033 0.001 PHEBB 38 TYR 0.046 0.001 TYRBD 123 ARG 0.017 0.000 ARGBd 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 684 time to evaluate : 4.053 Fit side-chains TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 205 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: BB 211 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.5917 (p90) REVERT: BC 81 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: BC 236 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.6198 (t80) REVERT: BC 255 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8365 (tm130) REVERT: BG 44 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: BH 28 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5880 (t80) REVERT: BI 7 MET cc_start: 0.7240 (tpt) cc_final: 0.6836 (tpt) REVERT: BI 78 LEU cc_start: 0.8971 (mp) cc_final: 0.8688 (mt) REVERT: BI 200 LEU cc_start: 0.9167 (tp) cc_final: 0.8809 (tp) REVERT: BN 38 THR cc_start: 0.8397 (m) cc_final: 0.8127 (p) REVERT: BO 53 LEU cc_start: 0.8167 (mm) cc_final: 0.7895 (tp) REVERT: BO 143 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7866 (ptmt) REVERT: BR 23 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4197 (ttm-80) REVERT: BR 58 MET cc_start: 0.7294 (mmm) cc_final: 0.6857 (mmm) REVERT: Bb 83 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7401 (ttm-80) REVERT: Be 25 ASP cc_start: 0.7849 (t0) cc_final: 0.7610 (t0) REVERT: BD 70 ARG cc_start: 0.4910 (OUTLIER) cc_final: 0.4589 (tmm160) REVERT: BD 160 MET cc_start: 0.7539 (tpp) cc_final: 0.7293 (tpt) REVERT: BD 192 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6913 (ttm) REVERT: BF 184 LEU cc_start: 0.8903 (mt) cc_final: 0.8588 (tm) REVERT: BK 46 MET cc_start: 0.4042 (tpt) cc_final: 0.3701 (tpt) REVERT: BP 39 LEU cc_start: 0.1777 (OUTLIER) cc_final: 0.1524 (pt) REVERT: BP 56 LYS cc_start: 0.2088 (OUTLIER) cc_final: 0.1020 (pttt) REVERT: BP 95 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4561 (pmt) REVERT: BQ 69 MET cc_start: 0.4518 (tpt) cc_final: 0.4157 (tpt) REVERT: BQ 129 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: BQ 136 ARG cc_start: 0.6256 (tpp-160) cc_final: 0.6027 (tpp80) REVERT: BS 54 LYS cc_start: 0.4312 (mttt) cc_final: 0.3430 (mppt) REVERT: BS 115 LYS cc_start: 0.4747 (pmtt) cc_final: 0.4476 (pmmt) REVERT: BT 5 ARG cc_start: 0.4056 (OUTLIER) cc_final: 0.2889 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6271 (t-90) cc_final: 0.5691 (t-170) REVERT: BT 55 TYR cc_start: 0.6913 (m-80) cc_final: 0.6657 (m-10) REVERT: BT 77 GLN cc_start: 0.7564 (tt0) cc_final: 0.7338 (tp-100) REVERT: BT 129 ARG cc_start: 0.5717 (ptm-80) cc_final: 0.5453 (tmm160) REVERT: BU 23 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.4926 (mtm180) REVERT: Bc 32 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6236 (p0) REVERT: Bd 37 MET cc_start: 0.7908 (mmm) cc_final: 0.7606 (mmm) REVERT: Bg 99 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7183 (mm) REVERT: Bg 141 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3507 (mp) REVERT: BZ 73 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5541 (p0) outliers start: 229 outliers final: 133 residues processed: 842 average time/residue: 1.4479 time to fit residues: 1610.2029 Evaluate side-chains 801 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 646 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 57 THR Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 203 ILE Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 23 VAL Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 28 PHE Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BI residue 38 SER Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 12 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BO residue 45 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BV residue 79 ILE Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 36 ASP Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 83 ARG Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 70 ARG Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 43 ILE Chi-restraints excluded: chain BP residue 39 LEU Chi-restraints excluded: chain BP residue 56 LYS Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BP residue 95 MET Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 62 SER Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BQ residue 129 GLU Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 85 ARG Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BU residue 23 ARG Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 60 GLU Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 326 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 28 ASN Chi-restraints excluded: chain BZ residue 66 LEU Chi-restraints excluded: chain BZ residue 71 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 76 GLU Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 544 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 412 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 475 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 562 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 163 GLN BG 65 GLN ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 3 HIS BJ 5 ASN BR 15 GLN ** BR 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN Be 29 GLN BQ 98 GLN BS 120 HIS BT 106 GLN ** Bd 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 73222 Z= 0.499 Angle : 0.834 17.633 106271 Z= 0.413 Chirality : 0.046 0.475 13064 Planarity : 0.006 0.144 7660 Dihedral : 23.186 179.962 29158 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.35 % Favored : 91.58 % Rotamer: Outliers : 7.87 % Allowed : 35.91 % Favored : 56.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4312 helix: 0.19 (0.14), residues: 1272 sheet: -0.63 (0.18), residues: 800 loop : -1.29 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPBT 53 HIS 0.010 0.001 HISBS 120 PHE 0.031 0.002 PHEBK 49 TYR 0.047 0.002 TYRBD 123 ARG 0.012 0.001 ARGBK 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 648 time to evaluate : 3.968 Fit side-chains TARDY: cannot create tardy model for: "LYSBE 7 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 197 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6276 (m-70) REVERT: BA 200 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5404 (mt-10) REVERT: BB 89 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7309 (mm-30) REVERT: BB 205 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: BC 81 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: BC 236 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.6982 (t80) REVERT: BC 255 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8394 (tm130) REVERT: BE 21 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7514 (p0) REVERT: BE 198 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8227 (mtp180) REVERT: BG 43 GLU cc_start: 0.8491 (pp20) cc_final: 0.8291 (pp20) REVERT: BG 44 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: BG 135 ARG cc_start: 0.6859 (tpt90) cc_final: 0.6553 (tpt90) REVERT: BI 7 MET cc_start: 0.7315 (tpt) cc_final: 0.6773 (tpt) REVERT: BI 10 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7308 (mtm180) REVERT: BI 78 LEU cc_start: 0.9017 (mp) cc_final: 0.8738 (mt) REVERT: BN 38 THR cc_start: 0.8553 (m) cc_final: 0.8307 (p) REVERT: BO 53 LEU cc_start: 0.8224 (mm) cc_final: 0.7958 (tp) REVERT: BO 132 VAL cc_start: 0.9069 (m) cc_final: 0.8854 (t) REVERT: BO 143 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8121 (ptmt) REVERT: BR 23 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.3812 (ttm-80) REVERT: BR 58 MET cc_start: 0.7240 (mmm) cc_final: 0.6923 (mmm) REVERT: BX 118 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7054 (mtp85) REVERT: BY 37 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7797 (ptm160) REVERT: BY 92 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: Bb 83 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7387 (ttm-80) REVERT: Be 25 ASP cc_start: 0.7948 (t0) cc_final: 0.7611 (t0) REVERT: BD 70 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4832 (ttp-170) REVERT: BD 187 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7779 (pp) REVERT: BD 192 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6947 (ttm) REVERT: BP 95 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.4551 (pmt) REVERT: BQ 69 MET cc_start: 0.4618 (tpt) cc_final: 0.4240 (tpt) REVERT: BS 51 ASP cc_start: 0.6349 (OUTLIER) cc_final: 0.6125 (p0) REVERT: BS 54 LYS cc_start: 0.4480 (mttt) cc_final: 0.3562 (mppt) REVERT: BS 64 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.4787 (tpt) REVERT: BT 5 ARG cc_start: 0.4261 (OUTLIER) cc_final: 0.3016 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6192 (t-90) cc_final: 0.5875 (t-170) REVERT: BT 55 TYR cc_start: 0.6918 (m-80) cc_final: 0.6693 (m-10) REVERT: BU 23 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4913 (mtm180) REVERT: Bc 32 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6029 (p0) REVERT: Bc 62 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6580 (mtt-85) REVERT: Bd 22 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7754 (ttm110) REVERT: Bd 28 HIS cc_start: 0.5849 (OUTLIER) cc_final: 0.5493 (t-90) REVERT: Bg 99 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6736 (mm) REVERT: Bg 141 ILE cc_start: 0.3848 (OUTLIER) cc_final: 0.3595 (mp) REVERT: BZ 41 LEU cc_start: 0.2490 (OUTLIER) cc_final: 0.1532 (pp) REVERT: BZ 73 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5451 (p0) outliers start: 296 outliers final: 193 residues processed: 858 average time/residue: 1.4173 time to fit residues: 1617.2205 Evaluate side-chains 847 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 623 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 91 VAL Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 197 HIS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 200 GLU Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 86 LEU Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 185 VAL Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 125 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 180 THR Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 247 THR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 7 LYS Chi-restraints excluded: chain BE residue 16 SER Chi-restraints excluded: chain BE residue 21 ASP Chi-restraints excluded: chain BE residue 32 SER Chi-restraints excluded: chain BE residue 57 THR Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 78 THR Chi-restraints excluded: chain BE residue 141 THR Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 198 ARG Chi-restraints excluded: chain BE residue 225 VAL Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 247 THR Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 185 THR Chi-restraints excluded: chain BG residue 203 ILE Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 23 VAL Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 45 TYR Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BH residue 126 ILE Chi-restraints excluded: chain BH residue 129 ASP Chi-restraints excluded: chain BH residue 146 ASP Chi-restraints excluded: chain BI residue 10 ARG Chi-restraints excluded: chain BI residue 38 SER Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 99 ASN Chi-restraints excluded: chain BI residue 121 ILE Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BI residue 169 GLU Chi-restraints excluded: chain BJ residue 9 ASN Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 59 ARG Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 6 SER Chi-restraints excluded: chain BN residue 12 SER Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 66 VAL Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BN residue 96 VAL Chi-restraints excluded: chain BO residue 45 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 55 THR Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BV residue 7 ASP Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BV residue 63 ASP Chi-restraints excluded: chain BV residue 79 ILE Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 118 ARG Chi-restraints excluded: chain BY residue 11 THR Chi-restraints excluded: chain BY residue 37 ARG Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 92 GLU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 28 LYS Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 11 ASN Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 83 ARG Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Be residue 48 VAL Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 70 ARG Chi-restraints excluded: chain BD residue 81 ASN Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 187 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 32 HIS Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 51 SER Chi-restraints excluded: chain BP residue 88 ASN Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BP residue 95 MET Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 62 SER Chi-restraints excluded: chain BQ residue 71 ILE Chi-restraints excluded: chain BQ residue 92 SER Chi-restraints excluded: chain BQ residue 119 THR Chi-restraints excluded: chain BS residue 51 ASP Chi-restraints excluded: chain BS residue 64 MET Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 85 ARG Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BT residue 113 ILE Chi-restraints excluded: chain BT residue 116 VAL Chi-restraints excluded: chain BU residue 23 ARG Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 80 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bc residue 60 GLU Chi-restraints excluded: chain Bc residue 62 ARG Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 72 THR Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 197 THR Chi-restraints excluded: chain Bg residue 266 CYS Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 326 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 28 ASN Chi-restraints excluded: chain BZ residue 41 LEU Chi-restraints excluded: chain BZ residue 66 LEU Chi-restraints excluded: chain BZ residue 71 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 76 GLU Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 348 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 383 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 442 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 65 GLN BH 34 ASN ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BR 42 GLN ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN BQ 87 GLN BQ 98 GLN BS 120 HIS BT 77 GLN ** Bd 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 73222 Z= 0.179 Angle : 0.716 18.144 106271 Z= 0.360 Chirality : 0.037 0.394 13064 Planarity : 0.005 0.124 7660 Dihedral : 23.122 179.804 29158 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 6.01 % Allowed : 37.91 % Favored : 56.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4312 helix: 0.38 (0.15), residues: 1291 sheet: -0.50 (0.18), residues: 792 loop : -1.18 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPBT 53 HIS 0.011 0.001 HISBS 120 PHE 0.024 0.001 PHEBA 94 TYR 0.049 0.001 TYRBD 123 ARG 0.013 0.000 ARGBI 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 664 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 89 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7259 (mm-30) REVERT: BB 205 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: BB 211 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.6179 (p90) REVERT: BC 81 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: BC 236 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.6124 (t80) REVERT: BC 255 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8371 (tm130) REVERT: BG 44 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: BG 134 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5528 (ttm) REVERT: BI 7 MET cc_start: 0.7214 (tpt) cc_final: 0.6782 (tpt) REVERT: BI 78 LEU cc_start: 0.8981 (mp) cc_final: 0.8689 (mt) REVERT: BN 38 THR cc_start: 0.8352 (m) cc_final: 0.8082 (p) REVERT: BO 53 LEU cc_start: 0.8201 (mm) cc_final: 0.7901 (tp) REVERT: BO 143 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7840 (ptmt) REVERT: BR 23 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4035 (ttm-80) REVERT: BR 58 MET cc_start: 0.7271 (mmm) cc_final: 0.6856 (mmm) REVERT: BX 97 ASP cc_start: 0.7871 (t0) cc_final: 0.7485 (t0) REVERT: BD 70 ARG cc_start: 0.4630 (OUTLIER) cc_final: 0.3980 (tmm160) REVERT: BD 151 LYS cc_start: 0.6610 (pmtt) cc_final: 0.5353 (mttp) REVERT: BD 192 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6695 (ttm) REVERT: BF 184 LEU cc_start: 0.8884 (mt) cc_final: 0.8577 (tm) REVERT: BP 56 LYS cc_start: 0.2347 (OUTLIER) cc_final: 0.1359 (pttt) REVERT: BP 95 MET cc_start: 0.4808 (OUTLIER) cc_final: 0.4504 (pmt) REVERT: BQ 69 MET cc_start: 0.4403 (tpt) cc_final: 0.4018 (tpt) REVERT: BQ 136 ARG cc_start: 0.6222 (tpp-160) cc_final: 0.5990 (tpp80) REVERT: BS 54 LYS cc_start: 0.4222 (mttt) cc_final: 0.3360 (mppt) REVERT: BS 115 LYS cc_start: 0.4950 (pmtt) cc_final: 0.4632 (pmmt) REVERT: BT 5 ARG cc_start: 0.4083 (OUTLIER) cc_final: 0.2903 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6301 (t-90) cc_final: 0.5877 (t-170) REVERT: BU 93 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3618 (mp) REVERT: Bc 32 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6205 (p0) REVERT: Bd 22 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7805 (ttm110) REVERT: Bg 99 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7217 (mm) REVERT: Bg 141 ILE cc_start: 0.3756 (OUTLIER) cc_final: 0.3521 (mp) REVERT: BZ 41 LEU cc_start: 0.2576 (OUTLIER) cc_final: 0.1617 (pp) REVERT: BZ 51 ILE cc_start: 0.3554 (OUTLIER) cc_final: 0.2914 (mp) REVERT: BZ 73 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5548 (p0) outliers start: 226 outliers final: 142 residues processed: 822 average time/residue: 1.4181 time to fit residues: 1544.3140 Evaluate side-chains 800 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 637 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 91 VAL Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 87 CYS Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 180 THR Chi-restraints excluded: chain BC residue 217 SER Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 32 SER Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 78 THR Chi-restraints excluded: chain BE residue 141 THR Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 134 MET Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 23 VAL Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 45 TYR Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 89 SER Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 9 ASN Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 6 SER Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 66 VAL Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 11 THR Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 36 ASP Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 70 ARG Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BP residue 56 LYS Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BP residue 95 MET Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BT residue 113 ILE Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain BU residue 101 VAL Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 7 LEU Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bd residue 46 ASN Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 197 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 41 LEU Chi-restraints excluded: chain BZ residue 51 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 76 GLU Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 512 optimal weight: 8.9990 chunk 539 optimal weight: 0.9980 chunk 491 optimal weight: 30.0000 chunk 524 optimal weight: 6.9990 chunk 315 optimal weight: 0.9980 chunk 228 optimal weight: 0.0670 chunk 411 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 473 optimal weight: 30.0000 chunk 496 optimal weight: 9.9990 chunk 522 optimal weight: 1.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 14 GLN ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 163 GLN ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 15 GLN ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN Be 29 GLN ** BQ 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 120 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 73222 Z= 0.179 Angle : 0.714 18.188 106271 Z= 0.359 Chirality : 0.037 0.394 13064 Planarity : 0.005 0.126 7660 Dihedral : 23.044 179.856 29158 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 5.16 % Allowed : 38.84 % Favored : 56.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4312 helix: 0.46 (0.15), residues: 1289 sheet: -0.45 (0.18), residues: 794 loop : -1.16 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPBg 236 HIS 0.012 0.001 HISBS 120 PHE 0.038 0.001 PHEBK 49 TYR 0.053 0.002 TYRBD 123 ARG 0.013 0.000 ARGBI 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 662 time to evaluate : 4.182 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 89 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7265 (mm-30) REVERT: BB 185 VAL cc_start: 0.8791 (t) cc_final: 0.8527 (p) REVERT: BB 205 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: BB 211 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6034 (p90) REVERT: BC 67 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7244 (ttp) REVERT: BC 81 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: BC 236 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.6094 (t80) REVERT: BC 255 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8351 (tm130) REVERT: BE 21 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7345 (p0) REVERT: BG 44 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: BH 28 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5873 (t80) REVERT: BI 7 MET cc_start: 0.7186 (tpt) cc_final: 0.6681 (tpt) REVERT: BI 78 LEU cc_start: 0.8991 (mp) cc_final: 0.8691 (mt) REVERT: BL 21 LYS cc_start: 0.6933 (mppt) cc_final: 0.6657 (mtmm) REVERT: BN 45 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7650 (tp40) REVERT: BO 53 LEU cc_start: 0.8195 (mm) cc_final: 0.7911 (tp) REVERT: BO 143 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7834 (ptmt) REVERT: BR 23 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.3855 (ttm170) REVERT: BR 58 MET cc_start: 0.7369 (mmm) cc_final: 0.6939 (mmm) REVERT: BX 97 ASP cc_start: 0.7894 (t0) cc_final: 0.7515 (t0) REVERT: BD 70 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.4469 (tmm160) REVERT: BD 151 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.5294 (mttm) REVERT: BD 192 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6795 (ttm) REVERT: BF 184 LEU cc_start: 0.8842 (mt) cc_final: 0.8588 (tm) REVERT: BP 56 LYS cc_start: 0.2283 (OUTLIER) cc_final: 0.1365 (pttt) REVERT: BQ 69 MET cc_start: 0.4344 (tpt) cc_final: 0.3990 (tpt) REVERT: BQ 136 ARG cc_start: 0.6185 (tpp-160) cc_final: 0.5938 (tpp80) REVERT: BS 54 LYS cc_start: 0.4228 (mttt) cc_final: 0.3382 (mppt) REVERT: BS 62 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.3329 (pm20) REVERT: BS 115 LYS cc_start: 0.4893 (pmtt) cc_final: 0.4592 (pmmt) REVERT: BT 5 ARG cc_start: 0.3957 (OUTLIER) cc_final: 0.2850 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6071 (t-90) cc_final: 0.5631 (t-170) REVERT: BT 46 LEU cc_start: 0.7930 (tm) cc_final: 0.7727 (tp) REVERT: BT 55 TYR cc_start: 0.6918 (m-10) cc_final: 0.6696 (m-10) REVERT: BU 63 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7726 (ptmt) REVERT: BU 93 ILE cc_start: 0.3995 (OUTLIER) cc_final: 0.3463 (mp) REVERT: Bc 32 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6118 (p0) REVERT: Bd 22 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7829 (ttm110) REVERT: Bd 28 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.5450 (t-90) REVERT: Bg 99 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7204 (mm) REVERT: Bg 141 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3508 (mp) REVERT: BZ 51 ILE cc_start: 0.3499 (OUTLIER) cc_final: 0.2857 (mp) REVERT: BZ 73 ASP cc_start: 0.5940 (OUTLIER) cc_final: 0.5544 (p0) outliers start: 194 outliers final: 139 residues processed: 800 average time/residue: 1.4064 time to fit residues: 1495.9272 Evaluate side-chains 797 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 633 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 151 LYS Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 211 TYR Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 67 MET Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 21 ASP Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 142 TYR Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 203 ILE Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 28 PHE Chi-restraints excluded: chain BH residue 54 VAL Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BI residue 38 SER Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 121 ILE Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BI residue 169 GLU Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 9 ASN Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BL residue 17 LEU Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 6 SER Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 66 VAL Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 89 SER Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 43 SER Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 37 VAL Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 70 ARG Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 151 LYS Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 152 ILE Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BK residue 43 ILE Chi-restraints excluded: chain BP residue 56 LYS Chi-restraints excluded: chain BP residue 91 ILE Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BQ residue 71 ILE Chi-restraints excluded: chain BS residue 62 GLU Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 71 ILE Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BT residue 113 ILE Chi-restraints excluded: chain BT residue 116 VAL Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain BU residue 101 VAL Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bd residue 28 HIS Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 168 VAL Chi-restraints excluded: chain Bg residue 197 THR Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain Bg residue 330 ASP Chi-restraints excluded: chain BZ residue 51 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 76 GLU Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 344 optimal weight: 2.9990 chunk 554 optimal weight: 10.0000 chunk 338 optimal weight: 0.0170 chunk 263 optimal weight: 0.3980 chunk 385 optimal weight: 0.5980 chunk 581 optimal weight: 8.9990 chunk 535 optimal weight: 2.9990 chunk 463 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 163 GLN BG 148 ASN ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 111 GLN ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 21 ASN ** BW 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN ** BQ 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 120 HIS BT 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 73222 Z= 0.169 Angle : 0.708 18.070 106271 Z= 0.356 Chirality : 0.036 0.379 13064 Planarity : 0.005 0.123 7660 Dihedral : 22.990 179.629 29158 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 4.63 % Allowed : 39.66 % Favored : 55.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4312 helix: 0.48 (0.15), residues: 1281 sheet: -0.40 (0.18), residues: 787 loop : -1.17 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPBT 53 HIS 0.012 0.001 HISBS 120 PHE 0.027 0.001 PHEBB 38 TYR 0.028 0.001 TYRBJ 10 ARG 0.014 0.000 ARGBJ 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8624 Ramachandran restraints generated. 4312 Oldfield, 0 Emsley, 4312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 653 time to evaluate : 4.056 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNBH 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSBH 12 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEUBb 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METCn 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 197 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.5993 (m-70) REVERT: BB 185 VAL cc_start: 0.8797 (t) cc_final: 0.8553 (m) REVERT: BB 205 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: BC 81 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: BC 236 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.6199 (t80) REVERT: BC 255 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8259 (tm130) REVERT: BE 21 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7320 (p0) REVERT: BG 44 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: BG 134 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5425 (ttm) REVERT: BI 7 MET cc_start: 0.7241 (tpt) cc_final: 0.6757 (tpt) REVERT: BI 78 LEU cc_start: 0.8973 (mp) cc_final: 0.8696 (mt) REVERT: BL 21 LYS cc_start: 0.6959 (mppt) cc_final: 0.6653 (pttt) REVERT: BO 53 LEU cc_start: 0.8182 (mm) cc_final: 0.7916 (tp) REVERT: BO 143 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7756 (ptmt) REVERT: BR 23 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.3757 (ttm-80) REVERT: BX 97 ASP cc_start: 0.7986 (t0) cc_final: 0.7580 (t0) REVERT: Bb 83 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7488 (ttm-80) REVERT: BD 70 ARG cc_start: 0.4779 (OUTLIER) cc_final: 0.4220 (tmm160) REVERT: BD 151 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.5375 (mttm) REVERT: BD 192 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6645 (ttm) REVERT: BF 184 LEU cc_start: 0.8847 (mt) cc_final: 0.8565 (tm) REVERT: BK 24 LYS cc_start: 0.7028 (mptt) cc_final: 0.6777 (mmtm) REVERT: BQ 69 MET cc_start: 0.4257 (tpt) cc_final: 0.3851 (tpt) REVERT: BQ 136 ARG cc_start: 0.6147 (tpp-160) cc_final: 0.5878 (tpp80) REVERT: BS 54 LYS cc_start: 0.4293 (mttt) cc_final: 0.3459 (mppt) REVERT: BS 62 GLU cc_start: 0.4493 (OUTLIER) cc_final: 0.3274 (pm20) REVERT: BS 115 LYS cc_start: 0.4926 (pmtt) cc_final: 0.4625 (pmmt) REVERT: BT 5 ARG cc_start: 0.3792 (OUTLIER) cc_final: 0.2718 (mpp-170) REVERT: BT 22 HIS cc_start: 0.6116 (t-90) cc_final: 0.5687 (t-170) REVERT: BT 55 TYR cc_start: 0.6791 (m-10) cc_final: 0.6557 (m-10) REVERT: BU 63 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7605 (ptmt) REVERT: BU 93 ILE cc_start: 0.4025 (OUTLIER) cc_final: 0.3489 (mp) REVERT: Bc 27 ARG cc_start: 0.5848 (ptt180) cc_final: 0.5606 (ttp80) REVERT: Bc 32 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.6209 (p0) REVERT: Bd 22 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7654 (ttm110) REVERT: Bg 99 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7191 (mm) REVERT: Bg 141 ILE cc_start: 0.3714 (OUTLIER) cc_final: 0.3493 (mp) REVERT: BZ 51 ILE cc_start: 0.3599 (OUTLIER) cc_final: 0.2970 (mp) REVERT: BZ 73 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5513 (p0) outliers start: 174 outliers final: 130 residues processed: 768 average time/residue: 1.4392 time to fit residues: 1465.9152 Evaluate side-chains 789 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 636 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 21 MET Chi-restraints excluded: chain BA residue 50 ILE Chi-restraints excluded: chain BA residue 161 VAL Chi-restraints excluded: chain BA residue 177 CYS Chi-restraints excluded: chain BA residue 197 HIS Chi-restraints excluded: chain BA residue 199 TRP Chi-restraints excluded: chain BA residue 204 ASP Chi-restraints excluded: chain BB residue 25 THR Chi-restraints excluded: chain BB residue 72 ASP Chi-restraints excluded: chain BB residue 90 ASP Chi-restraints excluded: chain BB residue 105 PHE Chi-restraints excluded: chain BB residue 120 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 134 MET Chi-restraints excluded: chain BB residue 180 ASP Chi-restraints excluded: chain BB residue 205 PHE Chi-restraints excluded: chain BB residue 234 ASP Chi-restraints excluded: chain BC residue 81 GLN Chi-restraints excluded: chain BC residue 94 VAL Chi-restraints excluded: chain BC residue 153 VAL Chi-restraints excluded: chain BC residue 230 ASP Chi-restraints excluded: chain BC residue 236 TYR Chi-restraints excluded: chain BC residue 255 GLN Chi-restraints excluded: chain BE residue 21 ASP Chi-restraints excluded: chain BE residue 71 MET Chi-restraints excluded: chain BE residue 72 VAL Chi-restraints excluded: chain BE residue 142 TYR Chi-restraints excluded: chain BE residue 171 ASP Chi-restraints excluded: chain BE residue 236 VAL Chi-restraints excluded: chain BE residue 249 ILE Chi-restraints excluded: chain BG residue 21 ASP Chi-restraints excluded: chain BG residue 28 TYR Chi-restraints excluded: chain BG residue 44 GLU Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 91 ASN Chi-restraints excluded: chain BG residue 98 SER Chi-restraints excluded: chain BG residue 127 THR Chi-restraints excluded: chain BG residue 134 MET Chi-restraints excluded: chain BH residue 22 THR Chi-restraints excluded: chain BH residue 27 PHE Chi-restraints excluded: chain BH residue 62 VAL Chi-restraints excluded: chain BH residue 111 VAL Chi-restraints excluded: chain BH residue 118 THR Chi-restraints excluded: chain BH residue 129 ASP Chi-restraints excluded: chain BI residue 38 SER Chi-restraints excluded: chain BI residue 72 VAL Chi-restraints excluded: chain BI residue 76 THR Chi-restraints excluded: chain BI residue 91 VAL Chi-restraints excluded: chain BI residue 121 ILE Chi-restraints excluded: chain BI residue 154 LEU Chi-restraints excluded: chain BI residue 162 THR Chi-restraints excluded: chain BI residue 169 GLU Chi-restraints excluded: chain BJ residue 2 VAL Chi-restraints excluded: chain BJ residue 9 ASN Chi-restraints excluded: chain BJ residue 35 GLU Chi-restraints excluded: chain BJ residue 63 THR Chi-restraints excluded: chain BJ residue 78 LEU Chi-restraints excluded: chain BJ residue 93 ASP Chi-restraints excluded: chain BL residue 18 CYS Chi-restraints excluded: chain BL residue 114 SER Chi-restraints excluded: chain BL residue 119 VAL Chi-restraints excluded: chain BL residue 140 ASN Chi-restraints excluded: chain BN residue 24 SER Chi-restraints excluded: chain BN residue 32 ASP Chi-restraints excluded: chain BN residue 66 VAL Chi-restraints excluded: chain BN residue 67 THR Chi-restraints excluded: chain BN residue 69 SER Chi-restraints excluded: chain BN residue 80 LEU Chi-restraints excluded: chain BN residue 87 ASP Chi-restraints excluded: chain BO residue 40 THR Chi-restraints excluded: chain BO residue 48 SER Chi-restraints excluded: chain BO residue 56 ILE Chi-restraints excluded: chain BO residue 57 THR Chi-restraints excluded: chain BO residue 105 THR Chi-restraints excluded: chain BO residue 107 THR Chi-restraints excluded: chain BO residue 138 ASP Chi-restraints excluded: chain BO residue 143 LYS Chi-restraints excluded: chain BR residue 23 ARG Chi-restraints excluded: chain BR residue 66 VAL Chi-restraints excluded: chain BR residue 85 VAL Chi-restraints excluded: chain BR residue 94 ASP Chi-restraints excluded: chain BR residue 96 ILE Chi-restraints excluded: chain BV residue 13 VAL Chi-restraints excluded: chain BV residue 21 ASN Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 80 ASP Chi-restraints excluded: chain BW residue 90 THR Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BY residue 84 ASN Chi-restraints excluded: chain BY residue 85 LEU Chi-restraints excluded: chain BY residue 97 LEU Chi-restraints excluded: chain BY residue 123 ILE Chi-restraints excluded: chain BY residue 129 THR Chi-restraints excluded: chain Ba residue 18 VAL Chi-restraints excluded: chain Ba residue 60 ASP Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 50 SER Chi-restraints excluded: chain Bb residue 83 ARG Chi-restraints excluded: chain Be residue 8 LEU Chi-restraints excluded: chain BD residue 20 PHE Chi-restraints excluded: chain BD residue 44 VAL Chi-restraints excluded: chain BD residue 45 THR Chi-restraints excluded: chain BD residue 70 ARG Chi-restraints excluded: chain BD residue 106 GLU Chi-restraints excluded: chain BD residue 151 LYS Chi-restraints excluded: chain BD residue 168 ASN Chi-restraints excluded: chain BD residue 170 TYR Chi-restraints excluded: chain BD residue 171 ILE Chi-restraints excluded: chain BD residue 192 MET Chi-restraints excluded: chain BD residue 214 HIS Chi-restraints excluded: chain BF residue 104 ILE Chi-restraints excluded: chain BF residue 164 LEU Chi-restraints excluded: chain BF residue 177 VAL Chi-restraints excluded: chain BF residue 198 SER Chi-restraints excluded: chain BK residue 37 VAL Chi-restraints excluded: chain BP residue 88 ASN Chi-restraints excluded: chain BQ residue 19 THR Chi-restraints excluded: chain BS residue 62 GLU Chi-restraints excluded: chain BS residue 67 LEU Chi-restraints excluded: chain BS residue 79 VAL Chi-restraints excluded: chain BT residue 5 ARG Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 37 ILE Chi-restraints excluded: chain BT residue 88 SER Chi-restraints excluded: chain BT residue 113 ILE Chi-restraints excluded: chain BU residue 63 LYS Chi-restraints excluded: chain BU residue 78 THR Chi-restraints excluded: chain BU residue 92 VAL Chi-restraints excluded: chain BU residue 93 ILE Chi-restraints excluded: chain BU residue 101 VAL Chi-restraints excluded: chain Bc residue 5 VAL Chi-restraints excluded: chain Bc residue 9 VAL Chi-restraints excluded: chain Bc residue 32 ASP Chi-restraints excluded: chain Bc residue 41 ASN Chi-restraints excluded: chain Bc residue 52 LEU Chi-restraints excluded: chain Bg residue 13 THR Chi-restraints excluded: chain Bg residue 21 VAL Chi-restraints excluded: chain Bg residue 82 VAL Chi-restraints excluded: chain Bg residue 86 ASP Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 114 VAL Chi-restraints excluded: chain Bg residue 120 VAL Chi-restraints excluded: chain Bg residue 133 VAL Chi-restraints excluded: chain Bg residue 134 SER Chi-restraints excluded: chain Bg residue 140 THR Chi-restraints excluded: chain Bg residue 141 ILE Chi-restraints excluded: chain Bg residue 168 VAL Chi-restraints excluded: chain Bg residue 269 THR Chi-restraints excluded: chain BZ residue 51 ILE Chi-restraints excluded: chain BZ residue 73 ASP Chi-restraints excluded: chain BZ residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 368 optimal weight: 20.0000 chunk 493 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 427 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 464 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 476 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 22 GLN BG 65 GLN BG 148 ASN ** BH 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 15 GLN ** BV 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 21 ASN BW 8 ASN ** BW 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 25 ASN Ba 94 ASN Bb 67 GLN ** BQ 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 120 HIS BT 106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105847 restraints weight = 140969.792| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.63 r_work: 0.3351 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 73222 Z= 0.383 Angle : 0.798 17.873 106271 Z= 0.397 Chirality : 0.042 0.468 13064 Planarity : 0.006 0.139 7660 Dihedral : 23.043 179.417 29158 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 5.37 % Allowed : 39.16 % Favored : 55.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.02 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4312 helix: 0.34 (0.15), residues: 1279 sheet: -0.55 (0.18), residues: 792 loop : -1.25 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRPBT 53 HIS 0.012 0.001 HISBS 120 PHE 0.036 0.002 PHEBD 155 TYR 0.056 0.002 TYRBD 123 ARG 0.014 0.001 ARGBI 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23129.79 seconds wall clock time: 401 minutes 51.05 seconds (24111.05 seconds total)