Starting phenix.real_space_refine on Mon Mar 25 13:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6f_18951/03_2024/8r6f_18951_updated.pdb" } resolution = 2.34 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= 0.007 sd= 0.134 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 14 8.98 5 Zn 1 6.06 5 P 1176 5.49 5 Mg 32 5.21 5 S 98 5.16 5 C 25619 2.51 5 N 8880 2.21 5 O 13196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 54": "OE1" <-> "OE2" Residue "Y GLU 92": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "X GLU 52": "OE1" <-> "OE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "k PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 60": "OE1" <-> "OE2" Residue "k GLU 122": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "I GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49016 Number of models: 1 Model: "" Number of chains: 39 Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "X" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1088 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2077 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "O" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" 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: "b" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "e" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 383 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain breaks: 1 Chain: "k" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1716 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain: "V" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 630 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "J" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1494 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1856 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "H" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1508 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "h" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 208 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "L" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1167 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "N" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1138 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1510 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 25190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 25190 Classifications: {'RNA': 1177} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 100, 'rna2p_pyr': 63, 'rna3p': 43, 'rna3p_pur': 530, 'rna3p_pyr': 429} Link IDs: {'rna2p': 165, 'rna3p': 1011} Chain breaks: 12 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 10 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Unusual residues: {' K': 14, ' MG': 31} Classifications: {'undetermined': 45} Link IDs: {None: 44} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 925 Classifications: {'water': 925} Link IDs: {None: 924} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11340 SG CYS a 23 107.708 158.515 90.171 1.00 28.06 S ATOM 11360 SG CYS a 26 104.892 157.857 92.140 1.00 30.55 S ATOM 11741 SG CYS a 74 104.721 157.381 88.703 1.00 22.96 S ATOM 11760 SG CYS a 77 104.435 160.782 90.366 1.00 23.83 S Time building chain proxies: 24.01, per 1000 atoms: 0.49 Number of scatterers: 49016 At special positions: 0 Unit cell: (171.14, 198.66, 141.9, 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 14 19.00 S 98 16.00 P 1176 15.00 Mg 32 11.99 O 13196 8.00 N 8880 7.00 C 25619 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: 26.01 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " Number of angles added : 6 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 33 sheets defined 30.8% alpha, 16.1% beta 338 base pairs and 587 stacking pairs defined. Time for finding SS restraints: 25.33 Creating SS restraints... Processing helix chain 'Y' and resid 42 through 53 Processing helix chain 'Y' and resid 58 through 60 No H-bonds generated for 'chain 'Y' and resid 58 through 60' Processing helix chain 'Y' and resid 85 through 91 Processing helix chain 'Y' and resid 94 through 100 Processing helix chain 'Y' and resid 110 through 121 Processing helix chain 'Y' and resid 126 through 128 No H-bonds generated for 'chain 'Y' and resid 126 through 128' Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.240A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA X 23 " --> pdb=" O ASN X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 34 through 37 Processing helix chain 'X' and resid 89 through 92 Processing helix chain 'X' and resid 129 through 133 Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 71 through 88 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 43 Processing helix chain 'W' and resid 83 through 93 removed outlier: 4.148A pdb=" N GLU W 87 " --> pdb=" O LYS W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'b' and resid 4 through 6 No H-bonds generated for 'chain 'b' and resid 4 through 6' Processing helix chain 'b' and resid 14 through 17 No H-bonds generated for 'chain 'b' and resid 14 through 17' Processing helix chain 'e' and resid 13 through 17 Processing helix chain 'e' and resid 33 through 44 Processing helix chain 'k' and resid 14 through 25 Processing helix chain 'k' and resid 55 through 71 Processing helix chain 'k' and resid 75 through 77 No H-bonds generated for 'chain 'k' and resid 75 through 77' Processing helix chain 'k' and resid 88 through 98 Processing helix chain 'k' and resid 135 through 143 removed outlier: 3.840A pdb=" N LEU k 143 " --> pdb=" O LYS k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 172 through 190 Processing helix chain 'k' and resid 204 through 206 No H-bonds generated for 'chain 'k' and resid 204 through 206' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 178 removed outlier: 3.589A pdb=" N SER B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'V' and resid 41 through 43 No H-bonds generated for 'chain 'V' and resid 41 through 43' Processing helix chain 'V' and resid 56 through 61 Processing helix chain 'V' and resid 64 through 79 Processing helix chain 'a' and resid 49 through 55 Processing helix chain 'a' and resid 75 through 80 Processing helix chain 'a' and resid 89 through 93 removed outlier: 4.213A pdb=" N ARG a 93 " --> pdb=" O ARG a 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 89 through 93' Processing helix chain 'J' and resid 4 through 7 Processing helix chain 'J' and resid 23 through 36 Processing helix chain 'J' and resid 41 through 62 removed outlier: 3.512A pdb=" N VAL J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 84 Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.532A pdb=" N LEU J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 95 through 99' Processing helix chain 'J' and resid 103 through 109 removed outlier: 3.718A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 117 Processing helix chain 'J' and resid 124 through 132 Processing helix chain 'J' and resid 152 through 157 removed outlier: 4.539A pdb=" N LYS J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N HIS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 157' Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 173 through 181 Processing helix chain 'C' and resid 50 through 57 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.705A pdb=" N VAL C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 231 removed outlier: 4.077A pdb=" N THR C 231 " --> pdb=" O CYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 249 through 252 No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.769A pdb=" N LEU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 156 through 162 removed outlier: 4.032A pdb=" N THR G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 228 Processing helix chain 'H' and resid 18 through 30 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 70 through 75 Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 115 through 117 No H-bonds generated for 'chain 'H' and resid 115 through 117' Processing helix chain 'H' and resid 119 through 130 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'h' and resid 100 through 108 Processing helix chain 'L' and resid 47 through 50 No H-bonds generated for 'chain 'L' and resid 47 through 50' Processing helix chain 'N' and resid 30 through 43 Processing helix chain 'N' and resid 47 through 56 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 90 through 93 No H-bonds generated for 'chain 'I' and resid 90 through 93' Processing helix chain 'I' and resid 108 through 118 Processing helix chain 'I' and resid 156 through 166 Processing helix chain 'I' and resid 174 through 181 removed outlier: 3.792A pdb=" N GLY I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 195 No H-bonds generated for 'chain 'I' and resid 192 through 195' Processing helix chain 'I' and resid 205 through 217 Processing sheet with id= A, first strand: chain 'Y' and resid 10 through 15 Processing sheet with id= B, first strand: chain 'Y' and resid 18 through 20 Processing sheet with id= C, first strand: chain 'X' and resid 79 through 83 removed outlier: 3.622A pdb=" N GLU X 52 " --> pdb=" O ARG X 70 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN X 72 " --> pdb=" O VAL X 50 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL X 50 " --> pdb=" O GLN X 72 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA X 102 " --> pdb=" O VAL X 121 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL X 121 " --> pdb=" O ALA X 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 89 through 92 removed outlier: 3.602A pdb=" N GLU E 97 " --> pdb=" O ILE E 92 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.632A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'E' and resid 225 through 227 removed outlier: 7.039A pdb=" N HIS E 209 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG E 198 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 52 through 57 removed outlier: 7.035A pdb=" N VAL O 44 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG O 55 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N HIS O 94 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= J, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.672A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE W 128 " --> pdb=" O TYR W 101 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'k' and resid 101 through 104 removed outlier: 3.668A pdb=" N SER k 82 " --> pdb=" O ILE k 103 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU k 125 " --> pdb=" O ILE k 79 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLN k 81 " --> pdb=" O LEU k 125 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE k 127 " --> pdb=" O GLN k 81 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU k 128 " --> pdb=" O PRO k 147 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE k 149 " --> pdb=" O LEU k 128 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE k 163 " --> pdb=" O ALA k 150 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS k 152 " --> pdb=" O ILE k 163 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE k 165 " --> pdb=" O CYS k 152 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'k' and resid 42 through 45 removed outlier: 6.741A pdb=" N ILE k 52 " --> pdb=" O TYR k 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= N, first strand: chain 'B' and resid 82 through 84 Processing sheet with id= O, first strand: chain 'B' and resid 86 through 88 Processing sheet with id= P, first strand: chain 'B' and resid 120 through 128 removed outlier: 3.945A pdb=" N LYS B 219 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG B 136 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= R, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= S, first strand: chain 'a' and resid 36 through 43 Processing sheet with id= T, first strand: chain 'J' and resid 136 through 138 Processing sheet with id= U, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.692A pdb=" N LYS C 92 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 113 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL C 90 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY C 115 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP C 88 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 168 through 172 Processing sheet with id= W, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.851A pdb=" N ILE G 49 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 72 through 78 Processing sheet with id= Y, first strand: chain 'G' and resid 164 through 167 Processing sheet with id= Z, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.631A pdb=" N GLY G 54 " --> pdb=" O ASN G 112 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 49 through 53 removed outlier: 3.516A pdb=" N ILE H 50 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 181 through 186 removed outlier: 4.206A pdb=" N ASP H 181 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'h' and resid 96 through 98 Processing sheet with id= AD, first strand: chain 'L' and resid 100 through 111 removed outlier: 6.032A pdb=" N ARG L 88 " --> pdb=" O CYS L 76 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS L 76 " --> pdb=" O ARG L 88 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN L 90 " --> pdb=" O GLY L 74 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY L 74 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 14.923A pdb=" N LEU L 92 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 16.246A pdb=" N ILE L 72 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY L 127 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL L 140 " --> pdb=" O GLY L 127 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 63 through 68 Processing sheet with id= AF, first strand: chain 'I' and resid 200 through 202 removed outlier: 3.601A pdb=" N ASP I 81 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP I 106 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU I 79 " --> pdb=" O ASP I 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 43 through 49 removed outlier: 6.552A pdb=" N ARG I 45 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA I 58 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL I 47 " --> pdb=" O TRP I 56 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP I 56 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL I 49 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL I 54 " --> pdb=" O VAL I 49 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 831 hydrogen bonds 1284 hydrogen bond angles 0 basepair planarities 338 basepair parallelities 587 stacking parallelities Total time for adding SS restraints: 59.45 Time building geometry restraints manager: 27.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4842 1.30 - 1.43: 20963 1.43 - 1.56: 22986 1.56 - 1.70: 2340 1.70 - 1.83: 153 Bond restraints: 51284 Sorted by residual: bond pdb=" C2' A2M A 545 " pdb=" C1' A2M A 545 " ideal model delta sigma weight residual 1.305 1.533 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' A2M A 440 " pdb=" C1' A2M A 440 " ideal model delta sigma weight residual 1.305 1.531 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2' A2M A 802 " pdb=" C1' A2M A 802 " ideal model delta sigma weight residual 1.305 1.531 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2' A2M A 468 " pdb=" C1' A2M A 468 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2' A2M A 623 " pdb=" C1' A2M A 623 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 51279 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.93: 5559 104.93 - 112.38: 28364 112.38 - 119.83: 19054 119.83 - 127.29: 19214 127.29 - 134.74: 2625 Bond angle restraints: 74816 Sorted by residual: angle pdb=" C1' A2M A 623 " pdb=" N9 A2M A 623 " pdb=" C8 A2M A 623 " ideal model delta sigma weight residual 88.50 128.56 -40.06 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C1' A2M A 979 " pdb=" N9 A2M A 979 " pdb=" C8 A2M A 979 " ideal model delta sigma weight residual 88.50 127.85 -39.35 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C1' A2M A 440 " pdb=" N9 A2M A 440 " pdb=" C8 A2M A 440 " ideal model delta sigma weight residual 88.50 127.70 -39.20 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C1' A2M A 424 " pdb=" N9 A2M A 424 " pdb=" C8 A2M A 424 " ideal model delta sigma weight residual 88.50 127.60 -39.10 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' A2M A 468 " pdb=" N9 A2M A 468 " pdb=" C8 A2M A 468 " ideal model delta sigma weight residual 88.50 127.59 -39.09 3.00e+00 1.11e-01 1.70e+02 ... (remaining 74811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 29010 35.89 - 71.79: 2983 71.79 - 107.68: 383 107.68 - 143.58: 9 143.58 - 179.47: 8 Dihedral angle restraints: 32393 sinusoidal: 24269 harmonic: 8124 Sorted by residual: dihedral pdb=" O4' C A 817 " pdb=" C1' C A 817 " pdb=" N1 C A 817 " pdb=" C2 C A 817 " ideal model delta sinusoidal sigma weight residual 200.00 46.26 153.74 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U A 816 " pdb=" C1' U A 816 " pdb=" N1 U A 816 " pdb=" C2 U A 816 " ideal model delta sinusoidal sigma weight residual -160.00 -8.65 -151.35 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' C A 791 " pdb=" C1' C A 791 " pdb=" N1 C A 791 " pdb=" C2 C A 791 " ideal model delta sinusoidal sigma weight residual 200.00 48.94 151.06 1 1.50e+01 4.44e-03 8.00e+01 ... (remaining 32390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 8366 0.075 - 0.150: 680 0.150 - 0.224: 103 0.224 - 0.299: 14 0.299 - 0.374: 8 Chirality restraints: 9171 Sorted by residual: chirality pdb=" CA AME V 1 " pdb=" N AME V 1 " pdb=" C AME V 1 " pdb=" CB AME V 1 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2' A2M A 424 " pdb=" C3' A2M A 424 " pdb=" O2' A2M A 424 " pdb=" C1' A2M A 424 " both_signs ideal model delta sigma weight residual False -2.39 -2.74 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' A2M A 28 " pdb=" C3' A2M A 28 " pdb=" O2' A2M A 28 " pdb=" C1' A2M A 28 " both_signs ideal model delta sigma weight residual False -2.39 -2.73 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 9168 not shown) Planarity restraints: 5146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A1131 " 0.045 2.00e-02 2.50e+03 5.97e-01 8.03e+03 pdb=" C4' OMG A1131 " 0.452 2.00e-02 2.50e+03 pdb=" O4' OMG A1131 " 0.693 2.00e-02 2.50e+03 pdb=" C3' OMG A1131 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMG A1131 " -0.604 2.00e-02 2.50e+03 pdb=" C2' OMG A1131 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG A1131 " 0.927 2.00e-02 2.50e+03 pdb=" C1' OMG A1131 " 0.211 2.00e-02 2.50e+03 pdb=" N9 OMG A1131 " -0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A 392 " 0.041 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMG A 392 " 0.450 2.00e-02 2.50e+03 pdb=" O4' OMG A 392 " 0.695 2.00e-02 2.50e+03 pdb=" C3' OMG A 392 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMG A 392 " -0.603 2.00e-02 2.50e+03 pdb=" C2' OMG A 392 " -0.205 2.00e-02 2.50e+03 pdb=" O2' OMG A 392 " 0.929 2.00e-02 2.50e+03 pdb=" C1' OMG A 392 " 0.212 2.00e-02 2.50e+03 pdb=" N9 OMG A 392 " -0.928 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A 38 " 0.064 2.00e-02 2.50e+03 5.95e-01 7.96e+03 pdb=" C4' OMC A 38 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMC A 38 " 0.608 2.00e-02 2.50e+03 pdb=" C3' OMC A 38 " -0.606 2.00e-02 2.50e+03 pdb=" O3' OMC A 38 " -0.639 2.00e-02 2.50e+03 pdb=" C2' OMC A 38 " -0.173 2.00e-02 2.50e+03 pdb=" O2' OMC A 38 " 0.983 2.00e-02 2.50e+03 pdb=" C1' OMC A 38 " 0.231 2.00e-02 2.50e+03 pdb=" N1 OMC A 38 " -0.896 2.00e-02 2.50e+03 ... (remaining 5143 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.47: 561 2.47 - 3.14: 37777 3.14 - 3.81: 117698 3.81 - 4.47: 170180 4.47 - 5.14: 226488 Nonbonded interactions: 552704 Sorted by model distance: nonbonded pdb="MG MG A1917 " pdb=" O HOH A2115 " model vdw 1.805 2.170 nonbonded pdb=" O2 PSU A 255 " pdb="MG MG A1918 " model vdw 1.818 2.170 nonbonded pdb=" OP2 A A 405 " pdb="MG MG A1933 " model vdw 1.850 2.170 nonbonded pdb=" OP1 G A 16 " pdb="MG MG A1927 " model vdw 1.853 2.170 nonbonded pdb=" OP2 G A 96 " pdb="MG MG A1929 " model vdw 1.859 2.170 ... (remaining 552699 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: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 24.180 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 187.780 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.009 0.228 51284 Z= 0.520 Angle : 0.999 40.056 74816 Z= 0.472 Chirality : 0.044 0.374 9171 Planarity : 0.024 0.597 5146 Dihedral : 22.484 179.472 27155 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.95 % Allowed : 18.89 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2786 helix: 0.58 (0.17), residues: 860 sheet: -0.23 (0.22), residues: 528 loop : 0.00 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 101 HIS 0.010 0.001 HIS N 123 PHE 0.029 0.002 PHE k 36 TYR 0.017 0.002 TYR V 45 ARG 0.011 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 489 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 69 ASP cc_start: 0.7979 (t70) cc_final: 0.7611 (t70) REVERT: V 73 GLN cc_start: 0.7642 (mt0) cc_final: 0.7290 (mt0) REVERT: G 43 GLU cc_start: 0.6454 (tp30) cc_final: 0.5922 (tp30) outliers start: 23 outliers final: 15 residues processed: 500 average time/residue: 2.0773 time to fit residues: 1239.4822 Evaluate side-chains 457 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 442 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN O 38 ASN W 8 ASN b 51 HIS k 76 GLN ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN k 136 GLN k 145 ASN B 63 HIS B 149 GLN a 11 ASN J 56 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN I 18 GLN I 194 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 51284 Z= 0.260 Angle : 0.789 18.271 74816 Z= 0.402 Chirality : 0.039 0.254 9171 Planarity : 0.008 0.138 5146 Dihedral : 23.130 170.214 21304 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.50 % Allowed : 18.48 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2786 helix: 1.02 (0.17), residues: 860 sheet: -0.30 (0.22), residues: 531 loop : 0.09 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 56 HIS 0.010 0.001 HIS b 51 PHE 0.024 0.002 PHE L 116 TYR 0.016 0.002 TYR E 58 ARG 0.008 0.001 ARG H 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 462 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6635 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7178 (mmtt) REVERT: Y 122 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8073 (mttt) REVERT: E 222 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8077 (tp) REVERT: O 75 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6357 (mtt) REVERT: B 152 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7390 (mtm180) REVERT: B 175 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: V 69 ASP cc_start: 0.7927 (t70) cc_final: 0.7418 (t70) REVERT: V 73 GLN cc_start: 0.7638 (mt0) cc_final: 0.7125 (mt0) REVERT: J 23 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7334 (mttt) REVERT: C 97 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: C 101 ARG cc_start: 0.7108 (tmt-80) cc_final: 0.6806 (tpt170) REVERT: H 156 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: N 106 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6637 (mtm-85) outliers start: 85 outliers final: 32 residues processed: 504 average time/residue: 2.0642 time to fit residues: 1243.6024 Evaluate side-chains 479 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 437 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 136 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 106 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 386 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN X 60 GLN E 62 GLN E 67 GLN k 81 GLN k 97 HIS k 136 GLN k 145 ASN B 28 GLN B 149 GLN a 11 ASN J 56 ASN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 HIS I 18 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 51284 Z= 0.475 Angle : 0.938 19.890 74816 Z= 0.464 Chirality : 0.047 0.280 9171 Planarity : 0.009 0.152 5146 Dihedral : 23.274 168.944 21283 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.49 % Allowed : 18.68 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2786 helix: 0.73 (0.17), residues: 866 sheet: -0.38 (0.22), residues: 546 loop : 0.00 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 56 HIS 0.008 0.002 HIS C 162 PHE 0.030 0.003 PHE Y 66 TYR 0.024 0.002 TYR E 58 ARG 0.010 0.001 ARG I 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 453 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6608 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7266 (mmtt) REVERT: E 222 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8213 (tp) REVERT: O 38 ASN cc_start: 0.7525 (m-40) cc_final: 0.7242 (m-40) REVERT: O 75 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: B 121 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 151 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7735 (ttmt) REVERT: B 175 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: V 69 ASP cc_start: 0.7999 (t70) cc_final: 0.7451 (t70) REVERT: V 73 GLN cc_start: 0.7698 (mt0) cc_final: 0.7151 (mt0) REVERT: J 23 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7354 (mttt) REVERT: J 66 GLU cc_start: 0.7075 (tp30) cc_final: 0.6803 (tp30) REVERT: J 104 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: C 97 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: C 101 ARG cc_start: 0.7077 (tmt-80) cc_final: 0.6823 (tpt170) REVERT: C 104 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: H 44 LEU cc_start: 0.7057 (tt) cc_final: 0.6662 (tp) REVERT: H 156 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6753 (m-30) REVERT: I 79 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (mt) outliers start: 109 outliers final: 54 residues processed: 514 average time/residue: 2.0576 time to fit residues: 1266.3404 Evaluate side-chains 510 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 443 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 18 MET Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 124 MET Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain N residue 111 SER Chi-restraints excluded: chain I residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 358 optimal weight: 2.9990 chunk 379 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 340 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN k 97 HIS k 136 GLN k 145 ASN B 149 GLN V 33 GLN a 11 ASN J 56 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 35 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 51284 Z= 0.303 Angle : 0.807 18.857 74816 Z= 0.411 Chirality : 0.040 0.282 9171 Planarity : 0.008 0.139 5146 Dihedral : 23.123 169.865 21283 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.57 % Allowed : 18.89 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2786 helix: 0.92 (0.17), residues: 866 sheet: -0.39 (0.22), residues: 541 loop : 0.07 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 56 HIS 0.008 0.001 HIS N 123 PHE 0.024 0.002 PHE L 35 TYR 0.024 0.002 TYR E 58 ARG 0.007 0.001 ARG Y 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 448 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6590 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7192 (mmtt) REVERT: X 14 LYS cc_start: 0.8102 (tttm) cc_final: 0.7659 (tptp) REVERT: E 222 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8188 (tp) REVERT: O 65 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: O 75 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6413 (mtt) REVERT: O 128 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6932 (mtp85) REVERT: e 23 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: k 31 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7411 (p) REVERT: B 121 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 175 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: B 231 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7452 (p) REVERT: V 8 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7400 (tmm) REVERT: V 69 ASP cc_start: 0.7983 (t70) cc_final: 0.7484 (t70) REVERT: V 73 GLN cc_start: 0.7720 (mt0) cc_final: 0.7266 (mt0) REVERT: J 66 GLU cc_start: 0.7072 (tp30) cc_final: 0.6821 (tp30) REVERT: J 104 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: C 97 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: C 101 ARG cc_start: 0.7080 (tmt-80) cc_final: 0.6838 (tpt170) REVERT: C 151 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8519 (mtm180) REVERT: C 232 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7465 (t80) REVERT: H 44 LEU cc_start: 0.7139 (tt) cc_final: 0.6666 (tp) REVERT: H 156 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: N 106 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6707 (mtm-85) outliers start: 111 outliers final: 51 residues processed: 506 average time/residue: 2.0620 time to fit residues: 1249.6244 Evaluate side-chains 504 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 435 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 136 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain V residue 8 MET Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 106 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN W 8 ASN k 97 HIS k 145 ASN B 149 GLN V 33 GLN a 11 ASN J 56 ASN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN G 148 ASN L 123 HIS N 123 HIS I 18 GLN I 35 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 51284 Z= 0.393 Angle : 0.873 19.423 74816 Z= 0.437 Chirality : 0.044 0.281 9171 Planarity : 0.008 0.146 5146 Dihedral : 23.168 169.646 21283 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.02 % Allowed : 18.81 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2786 helix: 0.89 (0.17), residues: 866 sheet: -0.48 (0.21), residues: 557 loop : 0.06 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 56 HIS 0.008 0.001 HIS N 123 PHE 0.028 0.002 PHE L 35 TYR 0.026 0.002 TYR E 58 ARG 0.010 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 445 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6599 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7265 (mmtt) REVERT: X 14 LYS cc_start: 0.8132 (tttm) cc_final: 0.7675 (tptp) REVERT: X 75 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7868 (pttt) REVERT: E 222 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8199 (tp) REVERT: O 75 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6419 (mtt) REVERT: O 128 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: e 23 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8223 (mtpt) REVERT: k 31 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7507 (p) REVERT: k 55 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7805 (mp) REVERT: B 103 MET cc_start: 0.8132 (ptt) cc_final: 0.7823 (ptt) REVERT: B 121 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8205 (mm) REVERT: B 151 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7742 (ttmt) REVERT: B 175 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: V 8 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7359 (tmm) REVERT: V 69 ASP cc_start: 0.7990 (t70) cc_final: 0.7629 (t70) REVERT: V 73 GLN cc_start: 0.7743 (mt0) cc_final: 0.7509 (mt0) REVERT: J 66 GLU cc_start: 0.7089 (tp30) cc_final: 0.6867 (tp30) REVERT: J 104 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: C 97 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: C 101 ARG cc_start: 0.7058 (tmt-80) cc_final: 0.6839 (tpt170) REVERT: C 215 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7944 (ptpp) REVERT: C 222 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: C 232 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7505 (t80) REVERT: H 44 LEU cc_start: 0.7222 (tt) cc_final: 0.6704 (tp) REVERT: H 156 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: N 106 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6727 (mtm-85) REVERT: I 19 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7438 (mmmm) outliers start: 122 outliers final: 65 residues processed: 522 average time/residue: 2.0271 time to fit residues: 1272.9516 Evaluate side-chains 523 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 437 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 55 LEU Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain V residue 8 MET Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain N residue 111 SER Chi-restraints excluded: chain I residue 19 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 380 optimal weight: 20.0000 chunk 315 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 199 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS k 136 GLN k 145 ASN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN V 33 GLN a 11 ASN J 56 ASN J 68 ASN G 148 ASN I 18 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 51284 Z= 0.191 Angle : 0.738 18.061 74816 Z= 0.382 Chirality : 0.036 0.270 9171 Planarity : 0.007 0.131 5146 Dihedral : 22.966 171.992 21283 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.87 % Allowed : 20.21 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2786 helix: 1.20 (0.18), residues: 875 sheet: -0.29 (0.22), residues: 536 loop : 0.17 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 113 HIS 0.009 0.001 HIS N 123 PHE 0.018 0.001 PHE L 35 TYR 0.023 0.001 TYR E 58 ARG 0.011 0.000 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 457 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 65 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7190 (mmtt) REVERT: X 14 LYS cc_start: 0.8072 (tttm) cc_final: 0.7633 (tptp) REVERT: E 66 MET cc_start: 0.8228 (tpp) cc_final: 0.7586 (mpp) REVERT: O 75 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6392 (mtt) REVERT: O 128 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6941 (mtp85) REVERT: O 142 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7432 (tpt-90) REVERT: W 36 LYS cc_start: 0.8559 (mttt) cc_final: 0.7947 (mttt) REVERT: k 31 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (p) REVERT: k 55 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 103 MET cc_start: 0.8036 (ptt) cc_final: 0.7722 (ptt) REVERT: B 175 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: V 69 ASP cc_start: 0.7985 (t70) cc_final: 0.7635 (t70) REVERT: J 66 GLU cc_start: 0.7100 (tp30) cc_final: 0.6890 (tp30) REVERT: C 88 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7136 (t70) REVERT: C 97 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: C 151 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8466 (mtm180) REVERT: C 232 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7538 (t80) REVERT: H 44 LEU cc_start: 0.7131 (tt) cc_final: 0.6634 (tp) REVERT: H 115 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6078 (mmt90) REVERT: H 156 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: N 106 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6604 (mtm-85) REVERT: I 19 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7475 (mmmm) outliers start: 94 outliers final: 44 residues processed: 511 average time/residue: 2.0963 time to fit residues: 1280.7323 Evaluate side-chains 495 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 437 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 122 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 35 GLU Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 55 LEU Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain N residue 111 SER Chi-restraints excluded: chain I residue 19 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 320 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 378 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN W 8 ASN b 5 ASN k 97 HIS k 135 HIS k 136 GLN k 145 ASN B 149 GLN V 33 GLN ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 ASN J 56 ASN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN L 123 HIS N 123 HIS I 18 GLN I 100 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 51284 Z= 0.509 Angle : 0.951 19.804 74816 Z= 0.467 Chirality : 0.048 0.284 9171 Planarity : 0.009 0.149 5146 Dihedral : 23.175 170.036 21281 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.69 % Allowed : 20.04 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2786 helix: 0.87 (0.17), residues: 866 sheet: -0.40 (0.22), residues: 556 loop : 0.03 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 56 HIS 0.009 0.002 HIS Y 69 PHE 0.031 0.003 PHE L 35 TYR 0.027 0.003 TYR E 58 ARG 0.012 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 434 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 18 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7436 (ptm) REVERT: Y 21 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6627 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7284 (mmtt) REVERT: X 14 LYS cc_start: 0.8175 (tttm) cc_final: 0.7700 (tptp) REVERT: E 222 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8117 (tp) REVERT: O 38 ASN cc_start: 0.7480 (m110) cc_final: 0.7259 (m-40) REVERT: O 75 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6379 (mtt) REVERT: O 128 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7037 (mtp85) REVERT: e 23 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8244 (mtpt) REVERT: k 31 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7568 (p) REVERT: k 135 HIS cc_start: 0.8359 (p90) cc_final: 0.8118 (p-80) REVERT: B 175 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: V 8 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7451 (tmm) REVERT: V 69 ASP cc_start: 0.8071 (t70) cc_final: 0.7817 (t70) REVERT: J 23 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7304 (mttt) REVERT: J 66 GLU cc_start: 0.7147 (tp30) cc_final: 0.6836 (tp30) REVERT: J 104 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 88 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7564 (t70) REVERT: C 97 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: C 151 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8568 (mtm180) REVERT: C 232 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7501 (t80) REVERT: H 44 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6573 (tp) REVERT: H 115 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6197 (mmt90) REVERT: H 156 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: N 106 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6778 (mtm-85) REVERT: I 19 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7424 (mmmm) outliers start: 114 outliers final: 69 residues processed: 503 average time/residue: 2.0724 time to fit residues: 1248.7876 Evaluate side-chains 516 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 426 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 18 MET Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 136 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain V residue 8 MET Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain N residue 111 SER Chi-restraints excluded: chain I residue 19 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 74 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN O 38 ASN b 67 GLN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS k 136 GLN k 145 ASN B 149 GLN V 33 GLN V 73 GLN a 11 ASN J 56 ASN J 68 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS I 18 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 51284 Z= 0.211 Angle : 0.757 18.247 74816 Z= 0.390 Chirality : 0.037 0.273 9171 Planarity : 0.007 0.133 5146 Dihedral : 22.989 171.747 21281 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.79 % Allowed : 21.03 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2786 helix: 1.11 (0.17), residues: 879 sheet: -0.28 (0.22), residues: 538 loop : 0.14 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 56 HIS 0.010 0.001 HIS N 123 PHE 0.020 0.002 PHE L 35 TYR 0.024 0.001 TYR E 58 ARG 0.013 0.000 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 448 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6580 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7179 (mmtt) REVERT: X 75 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7825 (pttt) REVERT: E 66 MET cc_start: 0.8210 (tpp) cc_final: 0.7610 (mpp) REVERT: E 222 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8058 (tp) REVERT: O 75 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6406 (mtt) REVERT: O 128 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6951 (mtp85) REVERT: O 142 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7468 (tpt-90) REVERT: k 31 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7486 (p) REVERT: k 55 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7815 (mp) REVERT: B 103 MET cc_start: 0.8068 (ptt) cc_final: 0.7712 (ptt) REVERT: B 121 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 175 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: V 69 ASP cc_start: 0.8088 (t70) cc_final: 0.7865 (t70) REVERT: V 73 GLN cc_start: 0.7752 (mt0) cc_final: 0.7550 (mt0) REVERT: J 66 GLU cc_start: 0.7099 (tp30) cc_final: 0.6824 (tp30) REVERT: C 88 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7195 (t70) REVERT: C 97 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: C 232 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7575 (t80) REVERT: G 214 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7532 (mp-120) REVERT: H 44 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6537 (tp) REVERT: H 115 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6069 (mmt90) REVERT: H 156 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: N 106 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6734 (mtm-85) REVERT: I 19 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7455 (mmmm) outliers start: 92 outliers final: 55 residues processed: 500 average time/residue: 2.0696 time to fit residues: 1241.0871 Evaluate side-chains 516 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 442 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 55 LEU Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 136 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain I residue 19 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 50.0000 chunk 362 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 333 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN E 130 GLN O 113 GLN W 8 ASN b 67 GLN k 97 HIS k 136 GLN k 145 ASN B 149 GLN V 33 GLN a 11 ASN J 56 ASN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS L 123 HIS N 123 HIS I 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 51284 Z= 0.565 Angle : 1.007 20.192 74816 Z= 0.491 Chirality : 0.050 0.287 9171 Planarity : 0.010 0.152 5146 Dihedral : 23.213 169.680 21281 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.91 % Allowed : 21.28 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2786 helix: 0.75 (0.17), residues: 869 sheet: -0.43 (0.22), residues: 550 loop : -0.04 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 56 HIS 0.012 0.002 HIS k 135 PHE 0.035 0.003 PHE k 36 TYR 0.027 0.003 TYR E 58 ARG 0.014 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 440 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 18 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7469 (ptm) REVERT: Y 21 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6637 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7292 (mmtt) REVERT: X 75 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (pttt) REVERT: E 222 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8016 (tp) REVERT: O 75 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6388 (mtt) REVERT: O 128 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7059 (mtp85) REVERT: e 26 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7501 (ptpp) REVERT: k 31 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7591 (p) REVERT: k 55 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7952 (mp) REVERT: B 175 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6656 (mp10) REVERT: V 69 ASP cc_start: 0.7982 (t70) cc_final: 0.7734 (t70) REVERT: C 88 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7597 (t70) REVERT: C 97 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: C 151 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8527 (mtm180) REVERT: C 232 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.7596 (t80) REVERT: G 214 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7584 (mp-120) REVERT: H 44 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6564 (tp) REVERT: H 115 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6264 (mmt90) REVERT: N 106 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6817 (mtm-85) REVERT: I 19 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7421 (mmmm) REVERT: I 79 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (mt) outliers start: 95 outliers final: 63 residues processed: 494 average time/residue: 2.1085 time to fit residues: 1245.2597 Evaluate side-chains 519 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 435 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 18 MET Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 27 GLN Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 26 MET Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 72 LYS Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 55 LEU Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 136 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 93 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.8980 chunk 373 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 259 optimal weight: 0.3980 chunk 391 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN O 38 ASN b 67 GLN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS k 135 HIS k 136 GLN k 145 ASN B 149 GLN V 33 GLN ** V 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN a 11 ASN J 56 ASN J 68 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS I 18 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 51284 Z= 0.174 Angle : 0.744 18.220 74816 Z= 0.386 Chirality : 0.036 0.273 9171 Planarity : 0.007 0.128 5146 Dihedral : 22.948 172.945 21281 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.13 % Allowed : 22.14 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2786 helix: 1.11 (0.17), residues: 877 sheet: -0.25 (0.22), residues: 536 loop : 0.16 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 113 HIS 0.011 0.001 HIS N 123 PHE 0.025 0.001 PHE k 36 TYR 0.022 0.001 TYR E 58 ARG 0.014 0.000 ARG I 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 449 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6581 (mtm-85) REVERT: Y 65 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7175 (mmtt) REVERT: X 14 LYS cc_start: 0.8057 (tttm) cc_final: 0.7633 (tptp) REVERT: X 75 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7816 (pttt) REVERT: E 222 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8072 (tp) REVERT: O 75 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6379 (mtt) REVERT: O 128 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6901 (mtp85) REVERT: W 36 LYS cc_start: 0.8560 (mttt) cc_final: 0.7975 (mttt) REVERT: k 31 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7541 (p) REVERT: k 84 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6945 (mtp-110) REVERT: B 175 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: V 69 ASP cc_start: 0.8093 (t70) cc_final: 0.7857 (t70) REVERT: V 73 GLN cc_start: 0.7752 (mt0) cc_final: 0.7520 (mt0) REVERT: C 97 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: C 232 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7626 (t80) REVERT: G 214 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (mp-120) REVERT: H 44 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6557 (tp) REVERT: H 115 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.5993 (mmt90) REVERT: H 156 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: N 106 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6659 (mtm-85) REVERT: I 19 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7457 (mmmm) outliers start: 76 outliers final: 46 residues processed: 493 average time/residue: 2.1291 time to fit residues: 1255.9874 Evaluate side-chains 503 residues out of total 2430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 441 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 21 ARG Chi-restraints excluded: chain Y residue 65 LYS Chi-restraints excluded: chain X residue 4 THR Chi-restraints excluded: chain X residue 21 ARG Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 54 ILE Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 128 ARG Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 35 MET Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 232 TYR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 106 ARG Chi-restraints excluded: chain I residue 19 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 0.0040 chunk 332 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 84 ASN b 5 ASN b 67 GLN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS k 136 GLN k 145 ASN B 149 GLN B 209 ASN V 33 GLN a 11 ASN J 56 ASN J 68 ASN G 26 ASN L 123 HIS N 123 HIS I 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132509 restraints weight = 43967.646| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 0.90 r_work: 0.3395 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 51284 Z= 0.379 Angle : 0.862 19.436 74816 Z= 0.432 Chirality : 0.043 0.280 9171 Planarity : 0.008 0.143 5146 Dihedral : 23.039 170.705 21281 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.13 % Allowed : 22.43 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2786 helix: 0.96 (0.17), residues: 871 sheet: -0.33 (0.21), residues: 560 loop : 0.11 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 56 HIS 0.012 0.002 HIS N 123 PHE 0.036 0.002 PHE k 36 TYR 0.027 0.002 TYR E 58 ARG 0.015 0.001 ARG I 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18828.62 seconds wall clock time: 335 minutes 0.94 seconds (20100.94 seconds total)