Starting phenix.real_space_refine on Sat Mar 23 05:32:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wav_37406/03_2024/8wav_37406_trim_updated.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.115 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 Zn 8 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22159 2.51 5 N 6274 2.21 5 O 6959 1.98 5 H 23 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35741 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 87 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'CSX:plan-1': 1, 'HYP:plan-1': 1, 'ILX:plan-1': 1, 'TRX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "X" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 879 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1111 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 261 Unusual residues: {'ATP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 9, None: 1} Not linked: pdbres="ATP Z 1 " pdbres=" U Z 2 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "o" Number of atoms: 11510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11510 Classifications: {'peptide': 1452} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1381} Chain breaks: 1 Chain: "p" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9149 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 53, 'TRANS': 1092} Chain breaks: 1 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "y" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, 'W0F': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4729 SG CYS o 71 113.996 112.506 115.179 1.00141.57 S ATOM 4751 SG CYS o 74 111.760 115.441 115.223 1.00137.29 S ATOM 4798 SG CYS o 81 110.347 111.834 114.992 1.00138.71 S ATOM 5033 SG CYS o 111 101.645 111.280 68.363 1.00164.45 S ATOM 5061 SG CYS o 114 103.694 114.625 68.038 1.00163.67 S ATOM 5407 SG CYS o 184 103.773 111.987 65.255 1.00171.81 S ATOM 24494 SG CYS p1119 105.495 124.974 104.025 1.00141.59 S ATOM 24516 SG CYS p1122 105.471 121.818 101.837 1.00142.57 S ATOM 24631 SG CYS p1137 108.320 122.474 104.008 1.00148.67 S ATOM 24652 SG CYS p1140 107.820 124.338 100.753 1.00152.98 S ATOM 25618 SG CYS q 88 85.466 90.662 173.481 1.00138.12 S ATOM 25631 SG CYS q 90 88.926 89.819 172.315 1.00147.15 S ATOM 25666 SG CYS q 94 87.099 87.421 174.624 1.00132.97 S ATOM 25688 SG CYS q 97 85.686 87.760 171.217 1.00132.45 S ATOM 32994 SG CYS w 17 75.494 52.501 55.824 1.00161.53 S ATOM 33018 SG CYS w 20 78.882 53.598 57.386 1.00163.91 S ATOM 33179 SG CYS w 39 76.726 56.245 56.465 1.00169.29 S ATOM 33204 SG CYS w 42 78.090 54.021 53.700 1.00167.79 S ATOM 33556 SG CYS w 86 44.290 43.172 86.125 1.00150.39 S ATOM 33580 SG CYS w 89 44.852 39.741 87.860 1.00155.57 S ATOM 33784 SG CYS w 114 46.591 42.868 89.120 1.00146.35 S ATOM 33819 SG CYS w 119 47.394 41.270 85.684 1.00152.45 S ATOM 33929 SG CYS x 7 65.620 72.431 151.683 1.00 98.61 S ATOM 33953 SG CYS x 10 64.018 73.325 154.895 1.00 95.35 S ATOM 34217 SG CYS x 44 61.792 72.456 151.693 1.00107.46 S ATOM 34223 SG CYS x 45 63.402 70.079 154.028 1.00108.23 S ATOM 35369 SG CYS z 19 107.137 61.301 142.340 1.00146.64 S ATOM 35388 SG CYS z 22 108.024 58.706 144.834 1.00145.85 S ATOM 35505 SG CYS z 36 110.746 61.257 143.910 1.00153.01 S ATOM 35531 SG CYS z 39 109.446 58.892 141.270 1.00150.68 S Time building chain proxies: 18.65, per 1000 atoms: 0.52 Number of scatterers: 35741 At special positions: 0 Unit cell: (165.416, 185.426, 192.096, 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 8 29.99 S 203 16.00 P 114 15.00 Mg 1 11.99 O 6959 8.00 N 6274 7.00 C 22159 6.00 H 23 1.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.41 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1202 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1140 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1119 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 43 sheets defined 32.3% alpha, 14.9% beta 37 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 14.57 Creating SS restraints... Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 157 through 165 Processing helix chain 'S' and resid 173 through 179 Processing helix chain 'T' and resid 10 through 14 Processing helix chain 'T' and resid 25 through 34 removed outlier: 4.166A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.238A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.871A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 236 Processing helix chain 'o' and resid 245 through 248 No H-bonds generated for 'chain 'o' and resid 245 through 248' Processing helix chain 'o' and resid 275 through 296 Processing helix chain 'o' and resid 302 through 318 Processing helix chain 'o' and resid 339 through 343 Processing helix chain 'o' and resid 349 through 352 No H-bonds generated for 'chain 'o' and resid 349 through 352' Processing helix chain 'o' and resid 382 through 387 Processing helix chain 'o' and resid 399 through 408 Processing helix chain 'o' and resid 435 through 438 removed outlier: 3.597A pdb=" N LEU o 438 " --> pdb=" O PRO o 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 435 through 438' Processing helix chain 'o' and resid 466 through 468 No H-bonds generated for 'chain 'o' and resid 466 through 468' Processing helix chain 'o' and resid 486 through 492 removed outlier: 4.160A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.864A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.931A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.221A pdb=" N SER o 615 " --> pdb=" O ASP o 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 611 through 615' Processing helix chain 'o' and resid 642 through 645 No H-bonds generated for 'chain 'o' and resid 642 through 645' Processing helix chain 'o' and resid 652 through 660 Processing helix chain 'o' and resid 662 through 683 Processing helix chain 'o' and resid 689 through 692 No H-bonds generated for 'chain 'o' and resid 689 through 692' Processing helix chain 'o' and resid 696 through 721 Processing helix chain 'o' and resid 733 through 759 Processing helix chain 'o' and resid 765 through 772 Processing helix chain 'o' and resid 778 through 785 Processing helix chain 'o' and resid 817 through 820 No H-bonds generated for 'chain 'o' and resid 817 through 820' Processing helix chain 'o' and resid 833 through 867 removed outlier: 4.424A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.139A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) Processing helix chain 'o' and resid 1121 through 1129 Processing helix chain 'o' and resid 1151 through 1161 Processing helix chain 'o' and resid 1166 through 1169 No H-bonds generated for 'chain 'o' and resid 1166 through 1169' Processing helix chain 'o' and resid 1188 through 1198 removed outlier: 3.744A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 1223 Processing helix chain 'o' and resid 1228 through 1239 Processing helix chain 'o' and resid 1263 through 1267 Processing helix chain 'o' and resid 1282 through 1295 Processing helix chain 'o' and resid 1343 through 1348 Processing helix chain 'o' and resid 1362 through 1369 Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1395 through 1406 Processing helix chain 'o' and resid 1416 through 1419 No H-bonds generated for 'chain 'o' and resid 1416 through 1419' Processing helix chain 'o' and resid 1426 through 1431 Processing helix chain 'o' and resid 1435 through 1445 removed outlier: 3.828A pdb=" N MET o1440 " --> pdb=" O ASP o1437 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'o' and resid 1477 through 1481 Processing helix chain 'p' and resid 22 through 36 removed outlier: 3.783A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 61 Processing helix chain 'p' and resid 110 through 115 Processing helix chain 'p' and resid 168 through 173 Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 281 through 288 Processing helix chain 'p' and resid 295 through 307 Proline residue: p 303 - end of helix Processing helix chain 'p' and resid 314 through 323 Processing helix chain 'p' and resid 332 through 345 Processing helix chain 'p' and resid 358 through 377 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'p' and resid 396 through 425 Processing helix chain 'p' and resid 431 through 434 No H-bonds generated for 'chain 'p' and resid 431 through 434' Processing helix chain 'p' and resid 437 through 450 Processing helix chain 'p' and resid 475 through 482 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 539 through 548 Processing helix chain 'p' and resid 580 through 593 Processing helix chain 'p' and resid 637 through 644 Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 667 through 672 removed outlier: 3.851A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 714 through 716 No H-bonds generated for 'chain 'p' and resid 714 through 716' Processing helix chain 'p' and resid 719 through 731 removed outlier: 3.736A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.573A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) Processing helix chain 'p' and resid 1055 through 1058 No H-bonds generated for 'chain 'p' and resid 1055 through 1058' Processing helix chain 'p' and resid 1088 through 1097 Processing helix chain 'p' and resid 1100 through 1111 removed outlier: 4.075A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p1111 " --> pdb=" O LEU p1107 " (cutoff:3.500A) Processing helix chain 'p' and resid 1153 through 1164 Processing helix chain 'q' and resid 28 through 40 Processing helix chain 'q' and resid 61 through 70 Processing helix chain 'q' and resid 78 through 81 No H-bonds generated for 'chain 'q' and resid 78 through 81' Processing helix chain 'q' and resid 117 through 119 No H-bonds generated for 'chain 'q' and resid 117 through 119' Processing helix chain 'q' and resid 174 through 176 No H-bonds generated for 'chain 'q' and resid 174 through 176' Processing helix chain 'q' and resid 200 through 202 No H-bonds generated for 'chain 'q' and resid 200 through 202' Processing helix chain 'q' and resid 241 through 270 removed outlier: 3.632A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 134 through 136 No H-bonds generated for 'chain 's' and resid 134 through 136' Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 15 through 27 removed outlier: 4.103A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA x 20 " --> pdb=" O LYS x 17 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.622A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.735A pdb=" N ASN x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 9 Processing helix chain 'y' and resid 40 through 52 removed outlier: 3.818A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.824A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.577A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.284A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU T 115 " --> pdb=" O LYS T 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 94 through 98 removed outlier: 3.600A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'o' and resid 86 through 89 Processing sheet with id= F, first strand: chain 'o' and resid 190 through 194 removed outlier: 4.618A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'o' and resid 264 through 266 Processing sheet with id= H, first strand: chain 'o' and resid 362 through 366 removed outlier: 3.529A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'o' and resid 367 through 369 removed outlier: 6.034A pdb=" N PHE o 482 " --> pdb=" O THR o 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'o' and resid 389 through 393 removed outlier: 3.931A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'o' and resid 602 through 604 removed outlier: 3.557A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU o 635 " --> pdb=" O GLU o 631 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'o' and resid 902 through 905 Processing sheet with id= M, first strand: chain 'o' and resid 1138 through 1142 removed outlier: 3.664A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 1244 through 1247 removed outlier: 4.365A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA o1174 " --> pdb=" O ARG o1213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id= P, first strand: chain 'p' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'p' and resid 91 through 93 removed outlier: 3.729A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE p 148 " --> pdb=" O VAL p 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'p' and resid 97 through 99 Processing sheet with id= S, first strand: chain 'p' and resid 185 through 187 Processing sheet with id= T, first strand: chain 'p' and resid 197 through 200 Processing sheet with id= U, first strand: chain 'p' and resid 205 through 208 removed outlier: 6.892A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= W, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.567A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'p' and resid 945 through 949 removed outlier: 6.915A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= Z, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AA, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AB, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.803A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.085A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 113 through 116 Processing sheet with id= AE, first strand: chain 's' and resid 60 through 62 removed outlier: 6.267A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 's' and resid 147 through 150 removed outlier: 3.653A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AH, first strand: chain 'u' and resid 2 through 13 Processing sheet with id= AI, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.007A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AK, first strand: chain 'u' and resid 44 through 48 removed outlier: 6.838A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.845A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.315A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AO, first strand: chain 'w' and resid 79 through 81 Processing sheet with id= AP, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AQ, first strand: chain 'z' and resid 16 through 18 1150 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 16.89 Time building geometry restraints manager: 16.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 23 1.17 - 1.33: 10382 1.33 - 1.49: 12054 1.49 - 1.66: 13858 1.66 - 1.82: 325 Bond restraints: 36642 Sorted by residual: bond pdb=" C3' ATP Z 1 " pdb=" O3' ATP Z 1 " ideal model delta sigma weight residual 1.423 1.639 -0.216 1.10e-02 8.26e+03 3.85e+02 bond pdb=" C4' G2L Z 12 " pdb=" C3' G2L Z 12 " ideal model delta sigma weight residual 1.270 1.521 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C2' G2L Z 12 " pdb=" C1' G2L Z 12 " ideal model delta sigma weight residual 1.271 1.520 -0.249 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C4 ATP Z 1 " pdb=" C5 ATP Z 1 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.07e+01 bond pdb=" O3' U Z 11 " pdb=" P G2L Z 12 " ideal model delta sigma weight residual 1.607 1.483 0.124 1.50e-02 4.44e+03 6.82e+01 ... (remaining 36637 not shown) Histogram of bond angle deviations from ideal: 75.34 - 89.88: 1 89.88 - 104.41: 1012 104.41 - 118.94: 29725 118.94 - 133.47: 19217 133.47 - 148.00: 42 Bond angle restraints: 49997 Sorted by residual: angle pdb=" PB ATP Z 1 " pdb=" O3B ATP Z 1 " pdb=" PG ATP Z 1 " ideal model delta sigma weight residual 139.87 120.69 19.18 1.00e+00 1.00e+00 3.68e+02 angle pdb=" C3' U Z 2 " pdb=" O3' U Z 2 " pdb=" P C Z 3 " ideal model delta sigma weight residual 120.20 148.00 -27.80 1.50e+00 4.44e-01 3.44e+02 angle pdb=" PA ATP Z 1 " pdb=" O3A ATP Z 1 " pdb=" PB ATP Z 1 " ideal model delta sigma weight residual 136.83 120.68 16.15 1.00e+00 1.00e+00 2.61e+02 angle pdb=" N09 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" O05 W0F p1201 " ideal model delta sigma weight residual 110.18 75.34 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C07 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " ideal model delta sigma weight residual 110.46 136.28 -25.82 3.00e+00 1.11e-01 7.41e+01 ... (remaining 49992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 21037 29.30 - 58.59: 1044 58.59 - 87.89: 64 87.89 - 117.19: 4 117.19 - 146.49: 1 Dihedral angle restraints: 22150 sinusoidal: 9990 harmonic: 12160 Sorted by residual: dihedral pdb=" CA TRP o 479 " pdb=" C TRP o 479 " pdb=" N SER o 480 " pdb=" CA SER o 480 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU o 343 " pdb=" C LEU o 343 " pdb=" N LYS o 344 " pdb=" CA LYS o 344 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA VAL o1341 " pdb=" C VAL o1341 " pdb=" N SER o1342 " pdb=" CA SER o1342 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 22147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4787 0.074 - 0.148: 743 0.148 - 0.222: 26 0.222 - 0.296: 3 0.296 - 0.370: 3 Chirality restraints: 5562 Sorted by residual: chirality pdb=" C06 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" O05 W0F p1201 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C03 W0F p1201 " pdb=" C04 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" O02 W0F p1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 5559 not shown) Planarity restraints: 6102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" C10 W0F p1201 " 0.041 2.00e-02 2.50e+03 pdb=" C12 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C17 W0F p1201 " -0.019 2.00e-02 2.50e+03 pdb=" N09 W0F p1201 " 0.051 2.00e-02 2.50e+03 pdb=" N11 W0F p1201 " 0.012 2.00e-02 2.50e+03 pdb=" N14 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F p1201 " -0.017 2.00e-02 2.50e+03 pdb=" N19 W0F p1201 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F p1201 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE p 51 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PHE p 50 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE p 51 " -0.023 2.00e-02 2.50e+03 ... (remaining 6099 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 42 2.39 - 2.94: 15937 2.94 - 3.49: 40817 3.49 - 4.05: 70762 4.05 - 4.60: 102576 Nonbonded interactions: 230134 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.832 2.050 nonbonded pdb=" C10 W0F p1201 " pdb=" O05 W0F p1201 " model vdw 1.871 2.520 nonbonded pdb=" OD1 ASP o 497 " pdb="MG MG o2003 " model vdw 1.916 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.019 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F p1201 " model vdw 2.039 2.800 ... (remaining 230129 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: 2.150 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: 0.870 Extract box with map and model: 8.420 Check model and map are aligned: 0.470 Set scattering table: 0.360 Process input model: 108.590 Find NCS groups from input model: 1.010 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 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 : 0.011 0.251 36619 Z= 0.690 Angle : 0.893 34.835 49945 Z= 0.472 Chirality : 0.051 0.370 5562 Planarity : 0.006 0.078 6098 Dihedral : 15.488 146.486 14277 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.92 % Favored : 95.89 % Rotamer: Outliers : 1.33 % Allowed : 5.88 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.34 (0.13), residues: 4137 helix: 1.08 (0.14), residues: 1421 sheet: 0.24 (0.20), residues: 652 loop : -0.31 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP o1192 HIS 0.010 0.001 HIS o 809 PHE 0.026 0.002 PHE o 548 TYR 0.035 0.002 TYR o 669 ARG 0.007 0.001 ARG p1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 944 time to evaluate : 3.893 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: symmetry clash REVERT: o 16 ARG cc_start: 0.7023 (mmt90) cc_final: 0.6447 (mtt-85) REVERT: o 18 ILE cc_start: 0.8471 (mt) cc_final: 0.8133 (mm) REVERT: o 30 GLU cc_start: 0.7153 (tt0) cc_final: 0.6853 (tt0) REVERT: o 58 MET cc_start: 0.7825 (ttp) cc_final: 0.7496 (mtp) REVERT: o 92 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7742 (mmmm) REVERT: o 120 ASP cc_start: 0.6914 (m-30) cc_final: 0.6638 (t0) REVERT: o 147 LEU cc_start: 0.6378 (mp) cc_final: 0.6108 (mp) REVERT: o 151 LYS cc_start: 0.6984 (mmtp) cc_final: 0.6583 (mmtp) REVERT: o 193 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7548 (ttt90) REVERT: o 196 LEU cc_start: 0.8195 (mt) cc_final: 0.7975 (mm) REVERT: o 197 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7099 (tp30) REVERT: o 215 LEU cc_start: 0.7391 (tp) cc_final: 0.6150 (tp) REVERT: o 219 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7272 (mp0) REVERT: o 229 SER cc_start: 0.6462 (t) cc_final: 0.5584 (p) REVERT: o 251 THR cc_start: 0.7800 (m) cc_final: 0.7534 (p) REVERT: o 274 ASP cc_start: 0.6213 (t0) cc_final: 0.5988 (t0) REVERT: o 316 THR cc_start: 0.6609 (m) cc_final: 0.6358 (p) REVERT: o 347 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7241 (mm-30) REVERT: o 382 ARG cc_start: 0.5975 (mtp-110) cc_final: 0.5437 (ttm110) REVERT: o 423 ASN cc_start: 0.7833 (m-40) cc_final: 0.7587 (p0) REVERT: o 470 MET cc_start: 0.8461 (mtm) cc_final: 0.8258 (mtp) REVERT: o 524 MET cc_start: 0.8094 (mmp) cc_final: 0.7843 (mmm) REVERT: o 552 ASP cc_start: 0.6650 (m-30) cc_final: 0.6255 (m-30) REVERT: o 556 GLU cc_start: 0.6381 (pt0) cc_final: 0.5597 (tp30) REVERT: o 561 MET cc_start: 0.7423 (mtt) cc_final: 0.7055 (mtt) REVERT: o 583 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6821 (ttp-110) REVERT: o 612 ASP cc_start: 0.6897 (m-30) cc_final: 0.6431 (p0) REVERT: o 700 GLN cc_start: 0.5793 (tt0) cc_final: 0.5456 (tp-100) REVERT: o 711 GLN cc_start: 0.6467 (tt0) cc_final: 0.6167 (mm-40) REVERT: o 714 ILE cc_start: 0.6800 (mt) cc_final: 0.6557 (mm) REVERT: o 726 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7543 (mp0) REVERT: o 794 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8220 (mm-30) REVERT: o 803 LYS cc_start: 0.7745 (tttp) cc_final: 0.7378 (tptp) REVERT: o 811 ILE cc_start: 0.6704 (mt) cc_final: 0.6277 (pt) REVERT: o 818 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7506 (mp0) REVERT: o 861 GLN cc_start: 0.6567 (tp40) cc_final: 0.6212 (mt0) REVERT: o 868 MET cc_start: 0.7440 (ptt) cc_final: 0.7057 (ptm) REVERT: o 919 LYS cc_start: 0.6612 (mttt) cc_final: 0.6232 (mmtm) REVERT: o 926 ASN cc_start: 0.7027 (m-40) cc_final: 0.6718 (t0) REVERT: o 936 GLU cc_start: 0.6836 (tt0) cc_final: 0.6289 (tm-30) REVERT: o 957 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6796 (mp0) REVERT: o 992 LYS cc_start: 0.7420 (mmtp) cc_final: 0.7158 (mmmm) REVERT: o 1132 LYS cc_start: 0.7057 (mmtt) cc_final: 0.6729 (mptt) REVERT: o 1133 LYS cc_start: 0.7288 (mttt) cc_final: 0.7040 (mmtm) REVERT: o 1135 LYS cc_start: 0.7951 (mttt) cc_final: 0.7647 (tptt) REVERT: o 1136 THR cc_start: 0.8746 (m) cc_final: 0.8477 (p) REVERT: o 1218 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7133 (ttm-80) REVERT: o 1219 LYS cc_start: 0.8549 (mttt) cc_final: 0.8085 (tppp) REVERT: o 1220 HIS cc_start: 0.6855 (m-70) cc_final: 0.6583 (m-70) REVERT: o 1259 ILE cc_start: 0.7690 (mt) cc_final: 0.7435 (mp) REVERT: o 1262 MET cc_start: 0.6457 (ttt) cc_final: 0.6197 (tpp) REVERT: o 1279 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6187 (tpp) REVERT: o 1295 ASP cc_start: 0.8220 (m-30) cc_final: 0.7992 (m-30) REVERT: o 1302 GLU cc_start: 0.7834 (pt0) cc_final: 0.7512 (mp0) REVERT: o 1306 LYS cc_start: 0.6580 (mttt) cc_final: 0.5969 (mtpt) REVERT: o 1310 HIS cc_start: 0.6367 (p-80) cc_final: 0.6141 (p90) REVERT: o 1321 ILE cc_start: 0.7583 (mt) cc_final: 0.7242 (pt) REVERT: o 1337 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5788 (mm-30) REVERT: o 1412 MET cc_start: 0.7207 (ttp) cc_final: 0.6742 (tmm) REVERT: o 1422 GLN cc_start: 0.7262 (mt0) cc_final: 0.5700 (mm110) REVERT: o 1428 MET cc_start: 0.6910 (ttm) cc_final: 0.6616 (ttm) REVERT: o 1452 LYS cc_start: 0.7488 (mttt) cc_final: 0.6892 (mmtm) REVERT: o 1472 ASP cc_start: 0.6795 (t0) cc_final: 0.6486 (t0) REVERT: o 1479 LYS cc_start: 0.5967 (ttmm) cc_final: 0.5733 (mtpt) REVERT: p 17 ILE cc_start: 0.8428 (mt) cc_final: 0.8016 (mm) REVERT: p 23 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6741 (tp40) REVERT: p 39 LEU cc_start: 0.8303 (mt) cc_final: 0.7950 (mm) REVERT: p 53 MET cc_start: 0.5254 (mmm) cc_final: 0.4994 (mmt) REVERT: p 215 TYR cc_start: 0.7076 (m-80) cc_final: 0.6677 (m-80) REVERT: p 239 MET cc_start: 0.7177 (ttm) cc_final: 0.6913 (ttp) REVERT: p 290 TYR cc_start: 0.7521 (m-80) cc_final: 0.7230 (m-80) REVERT: p 291 ASP cc_start: 0.6979 (t0) cc_final: 0.6220 (t0) REVERT: p 298 MET cc_start: 0.7515 (mmm) cc_final: 0.7231 (mtm) REVERT: p 299 GLU cc_start: 0.7972 (tp30) cc_final: 0.7714 (mm-30) REVERT: p 337 LYS cc_start: 0.5400 (tttm) cc_final: 0.5073 (mptt) REVERT: p 353 VAL cc_start: 0.7617 (m) cc_final: 0.7396 (p) REVERT: p 381 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7746 (mp0) REVERT: p 416 ARG cc_start: 0.6371 (mmm-85) cc_final: 0.5869 (ttm-80) REVERT: p 486 ASN cc_start: 0.8280 (t0) cc_final: 0.7296 (t0) REVERT: p 582 GLN cc_start: 0.7450 (mt0) cc_final: 0.6817 (tm-30) REVERT: p 606 ASP cc_start: 0.6112 (t0) cc_final: 0.5860 (t0) REVERT: p 682 LEU cc_start: 0.7120 (mp) cc_final: 0.6900 (mp) REVERT: p 728 MET cc_start: 0.7108 (mtm) cc_final: 0.6471 (mtp) REVERT: p 739 ASN cc_start: 0.7335 (p0) cc_final: 0.6727 (p0) REVERT: p 741 HIS cc_start: 0.7079 (t-90) cc_final: 0.6767 (p-80) REVERT: p 745 ASP cc_start: 0.7072 (m-30) cc_final: 0.6439 (m-30) REVERT: p 761 THR cc_start: 0.7880 (m) cc_final: 0.7562 (p) REVERT: p 768 ARG cc_start: 0.7111 (mmt180) cc_final: 0.6807 (mmm-85) REVERT: p 796 MET cc_start: 0.8800 (mtm) cc_final: 0.8317 (mtm) REVERT: p 816 GLU cc_start: 0.8009 (tp30) cc_final: 0.7564 (tp30) REVERT: p 850 ASP cc_start: 0.8171 (t0) cc_final: 0.7950 (p0) REVERT: p 911 LEU cc_start: 0.7531 (mt) cc_final: 0.7261 (mt) REVERT: p 993 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7609 (tttp) REVERT: p 1007 ASN cc_start: 0.7523 (m-40) cc_final: 0.7257 (m-40) REVERT: p 1043 ILE cc_start: 0.8518 (mt) cc_final: 0.8113 (tt) REVERT: p 1054 MET cc_start: 0.8347 (mtm) cc_final: 0.7780 (mtm) REVERT: p 1069 ILE cc_start: 0.8227 (mt) cc_final: 0.8011 (mp) REVERT: p 1080 ARG cc_start: 0.6644 (mtt90) cc_final: 0.6045 (mtp180) REVERT: p 1150 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7208 (mtp85) REVERT: p 1151 MET cc_start: 0.7647 (ptm) cc_final: 0.7369 (ptm) REVERT: p 1172 MET cc_start: 0.7480 (mmt) cc_final: 0.7025 (mmt) REVERT: q 17 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7166 (pt0) REVERT: q 93 PHE cc_start: 0.7328 (m-80) cc_final: 0.6625 (m-80) REVERT: q 102 THR cc_start: 0.8060 (m) cc_final: 0.7448 (p) REVERT: q 109 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5489 (pm20) REVERT: q 121 ILE cc_start: 0.8165 (mt) cc_final: 0.7957 (mm) REVERT: q 126 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6971 (mmm-85) REVERT: q 155 LYS cc_start: 0.6983 (tttt) cc_final: 0.6744 (tttm) REVERT: s 49 SER cc_start: 0.8371 (t) cc_final: 0.7680 (p) REVERT: s 57 ASP cc_start: 0.7640 (m-30) cc_final: 0.6835 (t0) REVERT: s 91 CYS cc_start: 0.7043 (t) cc_final: 0.6667 (t) REVERT: s 100 THR cc_start: 0.8124 (p) cc_final: 0.7807 (m) REVERT: s 133 GLN cc_start: 0.7363 (mt0) cc_final: 0.6863 (tp-100) REVERT: s 177 ASP cc_start: 0.7233 (t70) cc_final: 0.6937 (t70) REVERT: t 57 MET cc_start: 0.7822 (ttp) cc_final: 0.7546 (ttm) REVERT: t 61 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7223 (mt-10) REVERT: t 79 VAL cc_start: 0.7356 (t) cc_final: 0.6506 (m) REVERT: t 82 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7918 (pm20) REVERT: t 86 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6167 (mm-30) REVERT: t 114 SER cc_start: 0.6719 (t) cc_final: 0.5880 (p) REVERT: t 115 TYR cc_start: 0.7729 (p90) cc_final: 0.7500 (p90) REVERT: t 116 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7173 (mt-10) REVERT: u 45 VAL cc_start: 0.7266 (t) cc_final: 0.7048 (t) REVERT: u 53 ASN cc_start: 0.6425 (t0) cc_final: 0.5951 (p0) REVERT: u 104 MET cc_start: 0.7506 (ttp) cc_final: 0.6840 (ppp) REVERT: v 63 THR cc_start: 0.8995 (p) cc_final: 0.8564 (t) REVERT: v 71 ASP cc_start: 0.6784 (m-30) cc_final: 0.6341 (m-30) REVERT: v 76 ASN cc_start: 0.7421 (m-40) cc_final: 0.7198 (t160) REVERT: v 100 GLU cc_start: 0.7384 (tt0) cc_final: 0.6475 (mt-10) REVERT: v 110 THR cc_start: 0.7847 (p) cc_final: 0.6967 (p) REVERT: v 123 MET cc_start: 0.7850 (ttp) cc_final: 0.7579 (ttt) REVERT: v 126 GLN cc_start: 0.7778 (tt0) cc_final: 0.7511 (tt0) REVERT: v 133 HIS cc_start: 0.6684 (p-80) cc_final: 0.6369 (m170) REVERT: v 146 LYS cc_start: 0.6533 (tttt) cc_final: 0.6131 (tttm) REVERT: w 34 ILE cc_start: 0.7137 (mt) cc_final: 0.6904 (tt) REVERT: w 35 LEU cc_start: 0.7224 (tp) cc_final: 0.7021 (tp) REVERT: w 69 ILE cc_start: 0.7977 (mt) cc_final: 0.7672 (mp) REVERT: w 93 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6350 (mm-30) REVERT: w 115 THR cc_start: 0.6527 (m) cc_final: 0.5997 (p) REVERT: y 7 PHE cc_start: 0.6459 (p90) cc_final: 0.6137 (p90) REVERT: y 8 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7091 (mt-10) REVERT: y 23 LYS cc_start: 0.7908 (mttt) cc_final: 0.7567 (mttm) REVERT: y 32 LEU cc_start: 0.7630 (tp) cc_final: 0.7264 (mt) REVERT: y 53 ASP cc_start: 0.7276 (t70) cc_final: 0.7025 (t0) REVERT: y 93 ASP cc_start: 0.6776 (m-30) cc_final: 0.6428 (m-30) REVERT: z 25 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6920 (mp0) REVERT: z 35 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7306 (mtp85) outliers start: 49 outliers final: 14 residues processed: 979 average time/residue: 1.6669 time to fit residues: 1918.1019 Evaluate side-chains 610 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 595 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 1279 MET Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 432 GLU Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 903 ILE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain s residue 15 LYS Chi-restraints excluded: chain s residue 137 ILE Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 0.6980 chunk 319 optimal weight: 20.0000 chunk 177 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 329 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 382 optimal weight: 0.0670 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 181 HIS o 372 ASN o 377 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 531 ASN o 539 GLN o 671 ASN o 721 HIS o 731 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 945 ASN o 997 ASN o1032 GLN o1082 HIS o1105 ASN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN o1462 GLN p 43 GLN p 56 GLN p 117 ASN p 164 ASN p 245 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 518 HIS p 525 ASN ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 639 HIS p 699 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 838 GLN p 941 GLN p 948 GLN p1021 HIS p1068 GLN p1133 HIS q 18 ASN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN q 265 HIS r 66 ASN r 129 GLN s 64 HIS s 138 ASN t 46 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 53 ASN w 22 ASN w 50 ASN y 2 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 36619 Z= 0.156 Angle : 0.473 9.311 49945 Z= 0.255 Chirality : 0.039 0.178 5562 Planarity : 0.003 0.050 6098 Dihedral : 16.782 123.860 5850 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 2.79 % Allowed : 14.72 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.92 (0.13), residues: 4137 helix: 1.84 (0.14), residues: 1401 sheet: 0.25 (0.20), residues: 677 loop : -0.05 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP o1210 HIS 0.009 0.001 HIS r 43 PHE 0.016 0.001 PHE o 234 TYR 0.014 0.001 TYR o 669 ARG 0.006 0.000 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 631 time to evaluate : 3.959 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: o 16 ARG cc_start: 0.6972 (mmt90) cc_final: 0.6323 (mtt-85) REVERT: o 18 ILE cc_start: 0.8427 (mt) cc_final: 0.7998 (mm) REVERT: o 30 GLU cc_start: 0.7164 (tt0) cc_final: 0.6835 (tt0) REVERT: o 58 MET cc_start: 0.7789 (ttp) cc_final: 0.7549 (ttp) REVERT: o 92 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7739 (mmmm) REVERT: o 147 LEU cc_start: 0.6570 (mp) cc_final: 0.6327 (mp) REVERT: o 151 LYS cc_start: 0.6970 (mmtp) cc_final: 0.6581 (mptp) REVERT: o 193 ARG cc_start: 0.7909 (ttp80) cc_final: 0.6961 (ttt90) REVERT: o 196 LEU cc_start: 0.8224 (mt) cc_final: 0.8010 (mm) REVERT: o 197 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7203 (tp30) REVERT: o 220 ARG cc_start: 0.7364 (tpp80) cc_final: 0.6810 (mmm160) REVERT: o 226 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6769 (mtpt) REVERT: o 251 THR cc_start: 0.8132 (m) cc_final: 0.7876 (p) REVERT: o 274 ASP cc_start: 0.6243 (t0) cc_final: 0.5967 (t0) REVERT: o 295 GLN cc_start: 0.7802 (mt0) cc_final: 0.7516 (mp10) REVERT: o 316 THR cc_start: 0.7017 (m) cc_final: 0.6807 (p) REVERT: o 347 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7133 (mm-30) REVERT: o 382 ARG cc_start: 0.6089 (mtp-110) cc_final: 0.5581 (ttm110) REVERT: o 404 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5586 (tp30) REVERT: o 425 ASP cc_start: 0.6273 (m-30) cc_final: 0.6009 (p0) REVERT: o 470 MET cc_start: 0.8517 (mtm) cc_final: 0.8277 (mtp) REVERT: o 499 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: o 556 GLU cc_start: 0.6215 (pt0) cc_final: 0.5540 (tp30) REVERT: o 561 MET cc_start: 0.7493 (mtt) cc_final: 0.7181 (mtt) REVERT: o 583 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6988 (ttp-110) REVERT: o 612 ASP cc_start: 0.7085 (m-30) cc_final: 0.6530 (p0) REVERT: o 700 GLN cc_start: 0.6332 (tt0) cc_final: 0.5847 (tp-100) REVERT: o 711 GLN cc_start: 0.6510 (tt0) cc_final: 0.6194 (mm-40) REVERT: o 714 ILE cc_start: 0.6805 (mt) cc_final: 0.6560 (mm) REVERT: o 726 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7542 (mp0) REVERT: o 794 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8199 (mt-10) REVERT: o 803 LYS cc_start: 0.7755 (tttp) cc_final: 0.7319 (tptp) REVERT: o 818 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7425 (mp0) REVERT: o 861 GLN cc_start: 0.6595 (tp40) cc_final: 0.6125 (mt0) REVERT: o 868 MET cc_start: 0.7571 (ptt) cc_final: 0.7167 (ptm) REVERT: o 919 LYS cc_start: 0.6620 (mttt) cc_final: 0.6350 (mmtm) REVERT: o 936 GLU cc_start: 0.6627 (tt0) cc_final: 0.5714 (tp30) REVERT: o 1132 LYS cc_start: 0.7082 (mmtt) cc_final: 0.6835 (mptt) REVERT: o 1133 LYS cc_start: 0.7360 (mttt) cc_final: 0.7052 (mmtm) REVERT: o 1259 ILE cc_start: 0.7659 (mt) cc_final: 0.7423 (mp) REVERT: o 1262 MET cc_start: 0.6531 (ttt) cc_final: 0.6130 (tpp) REVERT: o 1279 MET cc_start: 0.6759 (mtm) cc_final: 0.6382 (tpp) REVERT: o 1286 ARG cc_start: 0.6511 (mtp85) cc_final: 0.6075 (mtp85) REVERT: o 1306 LYS cc_start: 0.6320 (mttt) cc_final: 0.5785 (mtpt) REVERT: o 1310 HIS cc_start: 0.6403 (p-80) cc_final: 0.5975 (p90) REVERT: o 1321 ILE cc_start: 0.7586 (mt) cc_final: 0.7325 (pt) REVERT: o 1337 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6013 (mm-30) REVERT: o 1376 LYS cc_start: 0.5787 (ttmm) cc_final: 0.5036 (tttt) REVERT: o 1412 MET cc_start: 0.7110 (ttp) cc_final: 0.6677 (tmm) REVERT: o 1422 GLN cc_start: 0.6822 (mt0) cc_final: 0.5490 (mm110) REVERT: o 1452 LYS cc_start: 0.7555 (mttt) cc_final: 0.6929 (mmtm) REVERT: o 1472 ASP cc_start: 0.6827 (t0) cc_final: 0.6582 (t0) REVERT: o 1479 LYS cc_start: 0.5935 (ttmm) cc_final: 0.5653 (mtpt) REVERT: p 23 GLN cc_start: 0.6898 (mm-40) cc_final: 0.6577 (tp40) REVERT: p 53 MET cc_start: 0.6150 (mmm) cc_final: 0.5912 (mmt) REVERT: p 87 LYS cc_start: 0.5875 (tttt) cc_final: 0.5523 (tptt) REVERT: p 215 TYR cc_start: 0.6794 (m-80) cc_final: 0.6389 (m-80) REVERT: p 239 MET cc_start: 0.7091 (ttm) cc_final: 0.6655 (ttp) REVERT: p 290 TYR cc_start: 0.7594 (m-80) cc_final: 0.7373 (m-80) REVERT: p 324 ARG cc_start: 0.6926 (mtt90) cc_final: 0.6442 (mtm-85) REVERT: p 381 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7720 (mp0) REVERT: p 416 ARG cc_start: 0.6413 (mmm-85) cc_final: 0.5990 (ttm-80) REVERT: p 486 ASN cc_start: 0.8131 (t0) cc_final: 0.7349 (t0) REVERT: p 508 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6007 (mtt) REVERT: p 606 ASP cc_start: 0.6196 (t0) cc_final: 0.5981 (t0) REVERT: p 677 MET cc_start: 0.8345 (tpp) cc_final: 0.7949 (tpp) REVERT: p 683 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6082 (mm-40) REVERT: p 728 MET cc_start: 0.7065 (mtm) cc_final: 0.6547 (mtp) REVERT: p 733 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7918 (ttm) REVERT: p 745 ASP cc_start: 0.6942 (m-30) cc_final: 0.6536 (m-30) REVERT: p 761 THR cc_start: 0.7745 (m) cc_final: 0.7521 (p) REVERT: p 796 MET cc_start: 0.8864 (mtm) cc_final: 0.8405 (mtm) REVERT: p 809 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.6952 (p) REVERT: p 816 GLU cc_start: 0.8345 (tp30) cc_final: 0.7776 (tp30) REVERT: p 846 ASP cc_start: 0.7944 (m-30) cc_final: 0.7681 (p0) REVERT: p 850 ASP cc_start: 0.8175 (t0) cc_final: 0.7940 (p0) REVERT: p 931 ILE cc_start: 0.7230 (pt) cc_final: 0.6912 (pp) REVERT: p 1007 ASN cc_start: 0.7339 (m-40) cc_final: 0.6961 (m-40) REVERT: p 1054 MET cc_start: 0.8426 (mtm) cc_final: 0.7916 (mtm) REVERT: p 1080 ARG cc_start: 0.6758 (mtt90) cc_final: 0.6224 (mtp180) REVERT: p 1106 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5991 (tpp-160) REVERT: p 1151 MET cc_start: 0.7550 (ptm) cc_final: 0.7121 (ptm) REVERT: p 1172 MET cc_start: 0.7492 (mmt) cc_final: 0.6992 (mmt) REVERT: q 17 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7192 (pt0) REVERT: q 24 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6784 (mt-10) REVERT: q 27 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: q 83 GLN cc_start: 0.8069 (mt0) cc_final: 0.7676 (mt0) REVERT: q 102 THR cc_start: 0.8017 (m) cc_final: 0.7487 (p) REVERT: q 109 GLU cc_start: 0.6392 (mt-10) cc_final: 0.5517 (pm20) REVERT: q 126 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7095 (mmm-85) REVERT: q 158 GLU cc_start: 0.6887 (tt0) cc_final: 0.6375 (pt0) REVERT: s 49 SER cc_start: 0.8066 (t) cc_final: 0.7620 (p) REVERT: s 57 ASP cc_start: 0.7155 (m-30) cc_final: 0.6941 (t0) REVERT: s 91 CYS cc_start: 0.7026 (t) cc_final: 0.6759 (m) REVERT: s 99 ILE cc_start: 0.7901 (mt) cc_final: 0.7667 (mp) REVERT: s 120 ASP cc_start: 0.6815 (m-30) cc_final: 0.6551 (m-30) REVERT: s 133 GLN cc_start: 0.7683 (mt0) cc_final: 0.7097 (tp-100) REVERT: s 137 ILE cc_start: 0.6860 (pt) cc_final: 0.6602 (pp) REVERT: s 159 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6655 (tm) REVERT: s 177 ASP cc_start: 0.7335 (t70) cc_final: 0.7009 (t70) REVERT: t 79 VAL cc_start: 0.6857 (t) cc_final: 0.6527 (m) REVERT: t 86 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5986 (mm-30) REVERT: t 112 ASP cc_start: 0.7145 (p0) cc_final: 0.6702 (p0) REVERT: t 114 SER cc_start: 0.6799 (t) cc_final: 0.6180 (p) REVERT: t 116 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7096 (mt-10) REVERT: u 53 ASN cc_start: 0.6420 (t0) cc_final: 0.6068 (p0) REVERT: u 158 PHE cc_start: 0.5952 (t80) cc_final: 0.5669 (t80) REVERT: v 4 ILE cc_start: 0.8257 (mt) cc_final: 0.7934 (mm) REVERT: v 26 SER cc_start: 0.7974 (p) cc_final: 0.7587 (m) REVERT: v 57 ARG cc_start: 0.6836 (ttp80) cc_final: 0.6594 (ttp80) REVERT: v 63 THR cc_start: 0.8936 (p) cc_final: 0.8557 (t) REVERT: v 71 ASP cc_start: 0.6605 (m-30) cc_final: 0.6059 (m-30) REVERT: v 76 ASN cc_start: 0.7282 (m-40) cc_final: 0.7027 (t160) REVERT: v 100 GLU cc_start: 0.7409 (tt0) cc_final: 0.6511 (mt-10) REVERT: v 126 GLN cc_start: 0.7763 (tt0) cc_final: 0.7504 (tt0) REVERT: v 145 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7417 (ttm) REVERT: v 146 LYS cc_start: 0.6523 (tttt) cc_final: 0.6085 (tttm) REVERT: w 69 ILE cc_start: 0.7843 (mt) cc_final: 0.7548 (mp) REVERT: w 93 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6376 (mm-30) REVERT: w 115 THR cc_start: 0.6411 (m) cc_final: 0.5847 (p) REVERT: y 16 GLU cc_start: 0.6657 (tt0) cc_final: 0.6155 (mt-10) REVERT: y 23 LYS cc_start: 0.8076 (mttt) cc_final: 0.7777 (mttp) REVERT: y 27 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8152 (p) REVERT: y 55 GLN cc_start: 0.7431 (mt0) cc_final: 0.6926 (mt0) REVERT: y 70 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7105 (ttmm) REVERT: y 93 ASP cc_start: 0.7017 (m-30) cc_final: 0.6724 (m-30) REVERT: z 25 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6960 (mp0) REVERT: z 35 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7688 (mtp85) outliers start: 103 outliers final: 39 residues processed: 690 average time/residue: 1.6506 time to fit residues: 1347.2055 Evaluate side-chains 610 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 561 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 404 GLU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 499 ASP Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1105 ASN Chi-restraints excluded: chain o residue 1159 CYS Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1222 THR Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 529 MET Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 733 MET Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1164 SER Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 89 THR Chi-restraints excluded: chain q residue 147 ASP Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain s residue 81 LYS Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 145 MET Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 307 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 372 ASN o 387 ASN o 449 HIS ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 486 ASN p 518 HIS ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 749 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 HIS u 14 HIS w 50 ASN w 98 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 36619 Z= 0.402 Angle : 0.606 11.584 49945 Z= 0.319 Chirality : 0.045 0.188 5562 Planarity : 0.005 0.057 6098 Dihedral : 16.647 121.199 5826 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 4.56 % Allowed : 15.67 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.43 (0.13), residues: 4137 helix: 1.34 (0.14), residues: 1405 sheet: -0.09 (0.19), residues: 695 loop : -0.25 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP o 479 HIS 0.009 0.002 HIS r 43 PHE 0.023 0.002 PHE p 402 TYR 0.022 0.002 TYR p 811 ARG 0.007 0.001 ARG p 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 573 time to evaluate : 3.915 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: symmetry clash REVERT: S 177 MET cc_start: 0.2397 (mmm) cc_final: 0.2140 (tpt) REVERT: o 16 ARG cc_start: 0.7145 (mmt90) cc_final: 0.6577 (mtt-85) REVERT: o 18 ILE cc_start: 0.8581 (mt) cc_final: 0.8206 (mm) REVERT: o 30 GLU cc_start: 0.6704 (tt0) cc_final: 0.6302 (tt0) REVERT: o 58 MET cc_start: 0.7876 (ttp) cc_final: 0.7488 (ttp) REVERT: o 115 SER cc_start: 0.7277 (p) cc_final: 0.6747 (t) REVERT: o 151 LYS cc_start: 0.6976 (mmtp) cc_final: 0.6728 (mptp) REVERT: o 193 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7391 (ttt90) REVERT: o 196 LEU cc_start: 0.8573 (mt) cc_final: 0.8259 (mt) REVERT: o 197 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6906 (pt0) REVERT: o 274 ASP cc_start: 0.6357 (t0) cc_final: 0.6051 (t0) REVERT: o 316 THR cc_start: 0.6776 (m) cc_final: 0.6466 (p) REVERT: o 321 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7323 (mt-10) REVERT: o 347 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7235 (mm-30) REVERT: o 382 ARG cc_start: 0.6896 (mtp-110) cc_final: 0.5751 (ttm110) REVERT: o 439 HIS cc_start: 0.6362 (t-90) cc_final: 0.6067 (t-90) REVERT: o 524 MET cc_start: 0.8345 (mmp) cc_final: 0.7488 (mmm) REVERT: o 556 GLU cc_start: 0.6351 (pt0) cc_final: 0.5759 (tp30) REVERT: o 583 ARG cc_start: 0.7302 (ptm160) cc_final: 0.7038 (ttp-110) REVERT: o 612 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6636 (p0) REVERT: o 700 GLN cc_start: 0.6591 (tt0) cc_final: 0.6045 (tp-100) REVERT: o 711 GLN cc_start: 0.6468 (tt0) cc_final: 0.6187 (mm-40) REVERT: o 726 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7718 (mp0) REVERT: o 803 LYS cc_start: 0.7712 (tttp) cc_final: 0.7386 (tptp) REVERT: o 818 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7359 (mp0) REVERT: o 845 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: o 861 GLN cc_start: 0.6725 (tp40) cc_final: 0.6061 (mt0) REVERT: o 919 LYS cc_start: 0.6730 (mttt) cc_final: 0.6455 (mmtm) REVERT: o 1168 LYS cc_start: 0.7888 (mttt) cc_final: 0.7457 (mtpt) REVERT: o 1259 ILE cc_start: 0.7488 (mt) cc_final: 0.7230 (mp) REVERT: o 1262 MET cc_start: 0.6401 (ttt) cc_final: 0.6149 (tpp) REVERT: o 1279 MET cc_start: 0.6811 (mtm) cc_final: 0.6420 (tpp) REVERT: o 1281 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7628 (t0) REVERT: o 1286 ARG cc_start: 0.6769 (mtp85) cc_final: 0.6317 (mtp85) REVERT: o 1306 LYS cc_start: 0.6034 (mttt) cc_final: 0.5690 (mtpt) REVERT: o 1310 HIS cc_start: 0.6274 (p-80) cc_final: 0.6050 (p90) REVERT: o 1337 GLU cc_start: 0.6331 (mt-10) cc_final: 0.6058 (mm-30) REVERT: o 1412 MET cc_start: 0.7693 (ttp) cc_final: 0.7286 (tmm) REVERT: o 1422 GLN cc_start: 0.6436 (mt0) cc_final: 0.5644 (mm110) REVERT: o 1452 LYS cc_start: 0.7447 (mttt) cc_final: 0.6611 (mmtm) REVERT: o 1484 MET cc_start: 0.3592 (ppp) cc_final: 0.3281 (ppp) REVERT: p 16 GLU cc_start: 0.5692 (mm-30) cc_final: 0.5426 (tp30) REVERT: p 53 MET cc_start: 0.6280 (mmm) cc_final: 0.5730 (mmm) REVERT: p 87 LYS cc_start: 0.6489 (tttt) cc_final: 0.6022 (tptt) REVERT: p 152 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7344 (mm) REVERT: p 160 TYR cc_start: 0.7131 (m-80) cc_final: 0.6814 (m-80) REVERT: p 198 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: p 215 TYR cc_start: 0.6852 (m-80) cc_final: 0.6141 (m-80) REVERT: p 239 MET cc_start: 0.6870 (ttm) cc_final: 0.6473 (ttp) REVERT: p 298 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6496 (mtp) REVERT: p 346 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5892 (mm-30) REVERT: p 381 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7717 (mp0) REVERT: p 416 ARG cc_start: 0.6430 (mmm-85) cc_final: 0.5960 (ttm-80) REVERT: p 420 GLN cc_start: 0.6189 (tt0) cc_final: 0.5861 (tp40) REVERT: p 438 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.5288 (ttp-110) REVERT: p 497 LYS cc_start: 0.7396 (tptp) cc_final: 0.7093 (tptt) REVERT: p 508 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6225 (mtt) REVERT: p 597 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7694 (mp) REVERT: p 728 MET cc_start: 0.7315 (mtm) cc_final: 0.6781 (mtp) REVERT: p 761 THR cc_start: 0.7752 (m) cc_final: 0.7412 (p) REVERT: p 771 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: p 796 MET cc_start: 0.8857 (mtm) cc_final: 0.8539 (mtm) REVERT: p 817 GLN cc_start: 0.8045 (pt0) cc_final: 0.7731 (pt0) REVERT: p 846 ASP cc_start: 0.8073 (m-30) cc_final: 0.7780 (p0) REVERT: p 850 ASP cc_start: 0.8218 (t0) cc_final: 0.7906 (p0) REVERT: p 863 ASP cc_start: 0.6788 (m-30) cc_final: 0.6385 (t0) REVERT: p 1007 ASN cc_start: 0.7577 (m-40) cc_final: 0.7339 (m-40) REVERT: p 1054 MET cc_start: 0.8455 (mtm) cc_final: 0.7913 (mtm) REVERT: p 1106 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6677 (mmp-170) REVERT: p 1136 GLU cc_start: 0.7746 (tt0) cc_final: 0.7449 (pt0) REVERT: p 1151 MET cc_start: 0.7788 (ptm) cc_final: 0.7300 (ptm) REVERT: p 1172 MET cc_start: 0.7572 (mmt) cc_final: 0.7180 (mmt) REVERT: q 17 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7363 (pt0) REVERT: q 18 ASN cc_start: 0.7612 (t0) cc_final: 0.6962 (t0) REVERT: q 20 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7050 (mtmt) REVERT: q 24 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6623 (mt-10) REVERT: q 27 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7890 (t70) REVERT: q 83 GLN cc_start: 0.7787 (mt0) cc_final: 0.7571 (mt0) REVERT: q 109 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6180 (pm20) REVERT: q 111 GLN cc_start: 0.7978 (tt0) cc_final: 0.7397 (mp10) REVERT: q 126 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7141 (mmm-85) REVERT: q 158 GLU cc_start: 0.7101 (tt0) cc_final: 0.6409 (pt0) REVERT: q 268 GLN cc_start: 0.7359 (mm-40) cc_final: 0.6759 (tm-30) REVERT: s 49 SER cc_start: 0.8232 (t) cc_final: 0.7808 (p) REVERT: s 91 CYS cc_start: 0.7075 (t) cc_final: 0.6853 (m) REVERT: s 120 ASP cc_start: 0.6852 (m-30) cc_final: 0.6596 (m-30) REVERT: s 133 GLN cc_start: 0.7768 (mt0) cc_final: 0.7296 (tp-100) REVERT: s 154 GLU cc_start: 0.6925 (mp0) cc_final: 0.6711 (mp0) REVERT: t 79 VAL cc_start: 0.6805 (t) cc_final: 0.6414 (t) REVERT: t 81 VAL cc_start: 0.6599 (t) cc_final: 0.5597 (m) REVERT: t 86 GLU cc_start: 0.6532 (mm-30) cc_final: 0.5953 (mm-30) REVERT: t 91 LEU cc_start: 0.6572 (mt) cc_final: 0.6232 (mt) REVERT: t 114 SER cc_start: 0.7126 (t) cc_final: 0.6537 (p) REVERT: u 104 MET cc_start: 0.5289 (tpp) cc_final: 0.4383 (tpt) REVERT: v 4 ILE cc_start: 0.8329 (mt) cc_final: 0.8104 (mm) REVERT: v 46 GLN cc_start: 0.8001 (mt0) cc_final: 0.7644 (tt0) REVERT: v 63 THR cc_start: 0.8999 (p) cc_final: 0.8624 (t) REVERT: v 71 ASP cc_start: 0.6732 (m-30) cc_final: 0.6253 (m-30) REVERT: v 74 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: v 76 ASN cc_start: 0.7397 (m-40) cc_final: 0.7183 (t0) REVERT: v 95 LYS cc_start: 0.7133 (tttt) cc_final: 0.6735 (ttpt) REVERT: v 100 GLU cc_start: 0.7479 (tt0) cc_final: 0.6638 (mt-10) REVERT: v 106 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7139 (t) REVERT: v 133 HIS cc_start: 0.7349 (p-80) cc_final: 0.6860 (m170) REVERT: v 141 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7399 (p) REVERT: w 18 GLN cc_start: 0.8267 (mt0) cc_final: 0.7932 (pp30) REVERT: w 68 ILE cc_start: 0.7478 (mt) cc_final: 0.7209 (mm) REVERT: w 69 ILE cc_start: 0.8193 (mt) cc_final: 0.7785 (mp) REVERT: w 71 ASP cc_start: 0.6899 (m-30) cc_final: 0.6603 (m-30) REVERT: w 93 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6284 (mm-30) REVERT: w 115 THR cc_start: 0.6338 (m) cc_final: 0.5798 (p) REVERT: x 19 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: x 57 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8013 (mm-30) REVERT: y 23 LYS cc_start: 0.8220 (mttt) cc_final: 0.7926 (mttm) REVERT: y 27 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8360 (p) REVERT: y 53 ASP cc_start: 0.7241 (t0) cc_final: 0.7005 (t0) REVERT: y 55 GLN cc_start: 0.7529 (mt0) cc_final: 0.7271 (mt0) REVERT: y 70 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7483 (ttmm) REVERT: y 93 ASP cc_start: 0.7216 (m-30) cc_final: 0.6824 (m-30) REVERT: z 25 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7094 (mp0) REVERT: z 35 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7483 (mtp85) REVERT: z 44 MET cc_start: 0.7983 (mmm) cc_final: 0.7678 (mmt) REVERT: z 56 ASP cc_start: 0.7436 (m-30) cc_final: 0.7028 (p0) outliers start: 168 outliers final: 71 residues processed: 673 average time/residue: 1.6101 time to fit residues: 1282.8503 Evaluate side-chains 623 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 534 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 116 LYS Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 407 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 550 LYS Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 852 VAL Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 957 GLU Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1031 ARG Chi-restraints excluded: chain o residue 1050 CYS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1159 CYS Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 590 LEU Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1133 HIS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 20 LYS Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 89 THR Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 0.7980 chunk 287 optimal weight: 0.4980 chunk 198 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 406 optimal weight: 0.0670 chunk 200 optimal weight: 1.9990 chunk 364 optimal weight: 0.0980 chunk 109 optimal weight: 0.6980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 301 HIS ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 950 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1163 HIS o1220 HIS p 265 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS q 18 ASN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 GLN u 53 ASN v 126 GLN w 22 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36619 Z= 0.124 Angle : 0.431 9.386 49945 Z= 0.233 Chirality : 0.038 0.166 5562 Planarity : 0.003 0.045 6098 Dihedral : 16.296 130.984 5826 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.21 % Favored : 96.64 % Rotamer: Outliers : 2.71 % Allowed : 18.71 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.91 (0.13), residues: 4137 helix: 1.97 (0.14), residues: 1400 sheet: 0.03 (0.19), residues: 688 loop : -0.09 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o 679 HIS 0.021 0.001 HIS p1133 PHE 0.017 0.001 PHE o 234 TYR 0.015 0.001 TYR p 388 ARG 0.006 0.000 ARG o 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 558 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: o 16 ARG cc_start: 0.6851 (mmt90) cc_final: 0.6358 (mtt-85) REVERT: o 18 ILE cc_start: 0.8530 (mt) cc_final: 0.8207 (mm) REVERT: o 30 GLU cc_start: 0.7231 (tt0) cc_final: 0.6831 (tt0) REVERT: o 58 MET cc_start: 0.7677 (ttp) cc_final: 0.7364 (ttp) REVERT: o 115 SER cc_start: 0.7268 (p) cc_final: 0.6786 (t) REVERT: o 151 LYS cc_start: 0.6965 (mmtp) cc_final: 0.6628 (mptp) REVERT: o 193 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7013 (ttt180) REVERT: o 196 LEU cc_start: 0.8498 (mt) cc_final: 0.8243 (mm) REVERT: o 197 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6827 (pt0) REVERT: o 199 TYR cc_start: 0.8023 (m-80) cc_final: 0.7612 (m-80) REVERT: o 220 ARG cc_start: 0.7369 (tpp80) cc_final: 0.6673 (mmm160) REVERT: o 223 GLU cc_start: 0.7632 (tp30) cc_final: 0.7291 (tp30) REVERT: o 274 ASP cc_start: 0.6328 (t0) cc_final: 0.6018 (t0) REVERT: o 316 THR cc_start: 0.6938 (m) cc_final: 0.6712 (p) REVERT: o 321 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7296 (mt-10) REVERT: o 347 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7261 (mm-30) REVERT: o 382 ARG cc_start: 0.6770 (mtp-110) cc_final: 0.5696 (ttm110) REVERT: o 517 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: o 524 MET cc_start: 0.8185 (mmp) cc_final: 0.7617 (mmm) REVERT: o 556 GLU cc_start: 0.6295 (pt0) cc_final: 0.5746 (tp30) REVERT: o 583 ARG cc_start: 0.7307 (ptm160) cc_final: 0.6930 (ttp-110) REVERT: o 612 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6597 (p0) REVERT: o 700 GLN cc_start: 0.6508 (tt0) cc_final: 0.5878 (tp-100) REVERT: o 711 GLN cc_start: 0.6441 (tt0) cc_final: 0.6195 (mm-40) REVERT: o 726 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7533 (mp0) REVERT: o 803 LYS cc_start: 0.7700 (tttp) cc_final: 0.7401 (tptp) REVERT: o 818 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7387 (mp0) REVERT: o 861 GLN cc_start: 0.6715 (tp40) cc_final: 0.6168 (mt0) REVERT: o 919 LYS cc_start: 0.6657 (mttt) cc_final: 0.6399 (mmtm) REVERT: o 1146 GLN cc_start: 0.7724 (pp30) cc_final: 0.7056 (pp30) REVERT: o 1168 LYS cc_start: 0.7841 (mttt) cc_final: 0.7406 (mtpt) REVERT: o 1259 ILE cc_start: 0.7427 (mt) cc_final: 0.7209 (mp) REVERT: o 1262 MET cc_start: 0.6418 (ttt) cc_final: 0.6194 (tpp) REVERT: o 1279 MET cc_start: 0.6707 (mtm) cc_final: 0.6333 (tpp) REVERT: o 1281 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7611 (t0) REVERT: o 1286 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6379 (mtp85) REVERT: o 1306 LYS cc_start: 0.6087 (mttt) cc_final: 0.5712 (mtpt) REVERT: o 1310 HIS cc_start: 0.6402 (p-80) cc_final: 0.5987 (p90) REVERT: o 1337 GLU cc_start: 0.6239 (mt-10) cc_final: 0.6002 (mm-30) REVERT: o 1376 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5636 (ttmm) REVERT: o 1412 MET cc_start: 0.7545 (ttp) cc_final: 0.7159 (tmm) REVERT: o 1422 GLN cc_start: 0.6453 (mt0) cc_final: 0.5240 (mm110) REVERT: o 1452 LYS cc_start: 0.7354 (mttt) cc_final: 0.6597 (mmtm) REVERT: o 1484 MET cc_start: 0.3399 (ppp) cc_final: 0.3141 (ppp) REVERT: p 16 GLU cc_start: 0.5620 (mm-30) cc_final: 0.5409 (tp30) REVERT: p 53 MET cc_start: 0.6214 (mmm) cc_final: 0.5606 (mmm) REVERT: p 87 LYS cc_start: 0.6134 (tttt) cc_final: 0.5649 (tptt) REVERT: p 160 TYR cc_start: 0.7124 (m-80) cc_final: 0.6854 (m-80) REVERT: p 215 TYR cc_start: 0.6899 (m-80) cc_final: 0.6126 (m-80) REVERT: p 239 MET cc_start: 0.6824 (ttm) cc_final: 0.6496 (ttp) REVERT: p 294 ASP cc_start: 0.7396 (p0) cc_final: 0.6453 (p0) REVERT: p 298 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6468 (mtp) REVERT: p 313 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6775 (tm-30) REVERT: p 346 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5931 (mm-30) REVERT: p 381 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7718 (mp0) REVERT: p 416 ARG cc_start: 0.6400 (mmm-85) cc_final: 0.5958 (ttm-80) REVERT: p 420 GLN cc_start: 0.6069 (tt0) cc_final: 0.5730 (tp40) REVERT: p 438 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5172 (ttp-110) REVERT: p 497 LYS cc_start: 0.7361 (tptp) cc_final: 0.7120 (tptt) REVERT: p 555 GLU cc_start: 0.7027 (pm20) cc_final: 0.6732 (tp30) REVERT: p 578 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7228 (mptt) REVERT: p 597 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7617 (mp) REVERT: p 683 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6414 (mp10) REVERT: p 728 MET cc_start: 0.7036 (mtm) cc_final: 0.6673 (mtp) REVERT: p 733 MET cc_start: 0.8119 (ttm) cc_final: 0.7878 (ttm) REVERT: p 761 THR cc_start: 0.7699 (m) cc_final: 0.7334 (p) REVERT: p 796 MET cc_start: 0.8807 (mtm) cc_final: 0.8507 (mtm) REVERT: p 809 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7147 (p) REVERT: p 817 GLN cc_start: 0.8068 (pt0) cc_final: 0.7759 (pt0) REVERT: p 846 ASP cc_start: 0.7992 (m-30) cc_final: 0.7732 (p0) REVERT: p 850 ASP cc_start: 0.8110 (t0) cc_final: 0.7891 (p0) REVERT: p 919 CYS cc_start: 0.8096 (t) cc_final: 0.7650 (p) REVERT: p 931 ILE cc_start: 0.7163 (pt) cc_final: 0.6831 (pp) REVERT: p 1151 MET cc_start: 0.7630 (ptm) cc_final: 0.7221 (ptm) REVERT: p 1172 MET cc_start: 0.7647 (mmt) cc_final: 0.7196 (mmt) REVERT: q 17 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7242 (pt0) REVERT: q 24 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6497 (mt-10) REVERT: q 109 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6174 (pm20) REVERT: q 111 GLN cc_start: 0.8029 (tt0) cc_final: 0.7270 (mp10) REVERT: q 126 ARG cc_start: 0.7512 (mtt180) cc_final: 0.7125 (mmm-85) REVERT: q 158 GLU cc_start: 0.7076 (tt0) cc_final: 0.6483 (pt0) REVERT: q 242 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: q 268 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6850 (tm-30) REVERT: s 49 SER cc_start: 0.8191 (t) cc_final: 0.7754 (p) REVERT: s 120 ASP cc_start: 0.6882 (m-30) cc_final: 0.6614 (m-30) REVERT: s 133 GLN cc_start: 0.7705 (mt0) cc_final: 0.7200 (tp-100) REVERT: s 159 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6565 (tm) REVERT: t 79 VAL cc_start: 0.6776 (t) cc_final: 0.6228 (t) REVERT: t 81 VAL cc_start: 0.6290 (t) cc_final: 0.5525 (m) REVERT: t 86 GLU cc_start: 0.6520 (mm-30) cc_final: 0.5942 (mm-30) REVERT: t 91 LEU cc_start: 0.6730 (mt) cc_final: 0.6450 (mt) REVERT: t 114 SER cc_start: 0.7153 (t) cc_final: 0.6651 (p) REVERT: u 53 ASN cc_start: 0.6365 (t0) cc_final: 0.6150 (p0) REVERT: u 104 MET cc_start: 0.5350 (tpp) cc_final: 0.4409 (tpt) REVERT: v 4 ILE cc_start: 0.8243 (mt) cc_final: 0.8007 (mm) REVERT: v 46 GLN cc_start: 0.7961 (mt0) cc_final: 0.7655 (tt0) REVERT: v 63 THR cc_start: 0.8947 (p) cc_final: 0.8601 (t) REVERT: v 71 ASP cc_start: 0.6659 (m-30) cc_final: 0.6175 (m-30) REVERT: v 74 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: v 76 ASN cc_start: 0.7272 (m-40) cc_final: 0.6947 (t0) REVERT: v 95 LYS cc_start: 0.7073 (tttt) cc_final: 0.6694 (ttpt) REVERT: v 100 GLU cc_start: 0.7474 (tt0) cc_final: 0.6630 (mt-10) REVERT: v 133 HIS cc_start: 0.7033 (p-80) cc_final: 0.6763 (m170) REVERT: w 18 GLN cc_start: 0.8290 (mt0) cc_final: 0.7765 (pp30) REVERT: w 44 TYR cc_start: 0.6919 (t80) cc_final: 0.6654 (t80) REVERT: w 47 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: w 68 ILE cc_start: 0.7461 (mt) cc_final: 0.7201 (mm) REVERT: w 69 ILE cc_start: 0.8042 (mt) cc_final: 0.7600 (mp) REVERT: w 71 ASP cc_start: 0.7456 (m-30) cc_final: 0.7131 (m-30) REVERT: w 93 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6255 (mm-30) REVERT: w 115 THR cc_start: 0.6105 (m) cc_final: 0.5463 (p) REVERT: x 57 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7818 (mm-30) REVERT: y 16 GLU cc_start: 0.6990 (tt0) cc_final: 0.6404 (mt-10) REVERT: y 23 LYS cc_start: 0.8188 (mttt) cc_final: 0.7862 (mttm) REVERT: y 27 VAL cc_start: 0.8526 (t) cc_final: 0.8304 (p) REVERT: y 53 ASP cc_start: 0.7210 (t0) cc_final: 0.6966 (t0) REVERT: y 55 GLN cc_start: 0.7473 (mt0) cc_final: 0.7128 (mt0) REVERT: y 70 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7250 (ttmm) REVERT: y 93 ASP cc_start: 0.7149 (m-30) cc_final: 0.6801 (m-30) REVERT: y 103 GLU cc_start: 0.6753 (tt0) cc_final: 0.6508 (tt0) REVERT: z 25 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7101 (mp0) REVERT: z 35 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7627 (mtp85) REVERT: z 44 MET cc_start: 0.7603 (mmm) cc_final: 0.7391 (mmt) REVERT: z 56 ASP cc_start: 0.7412 (m-30) cc_final: 0.7094 (p0) outliers start: 100 outliers final: 42 residues processed: 617 average time/residue: 1.6629 time to fit residues: 1214.3359 Evaluate side-chains 585 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 530 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 1031 ARG Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1159 CYS Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain p residue 266 GLU Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 435 ILE Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 683 GLN Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1164 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 242 GLU Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1105 ASN ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 265 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 941 GLN p 948 GLN p1133 HIS q 66 HIS q 83 GLN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 107 GLN s 108 GLN w 74 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 36619 Z= 0.474 Angle : 0.609 10.763 49945 Z= 0.319 Chirality : 0.045 0.174 5562 Planarity : 0.005 0.074 6098 Dihedral : 16.402 137.530 5826 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.85 % Rotamer: Outliers : 4.37 % Allowed : 17.90 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.34 (0.13), residues: 4137 helix: 1.40 (0.14), residues: 1388 sheet: -0.25 (0.19), residues: 700 loop : -0.36 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP q 49 HIS 0.010 0.002 HIS o1108 PHE 0.023 0.002 PHE q 63 TYR 0.024 0.002 TYR p 160 ARG 0.009 0.001 ARG p 924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 551 time to evaluate : 4.075 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: o 16 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6539 (mtt-85) REVERT: o 18 ILE cc_start: 0.8607 (mt) cc_final: 0.8259 (mm) REVERT: o 30 GLU cc_start: 0.6638 (tt0) cc_final: 0.6212 (tt0) REVERT: o 58 MET cc_start: 0.7800 (ttp) cc_final: 0.7436 (ttp) REVERT: o 115 SER cc_start: 0.7134 (p) cc_final: 0.6761 (t) REVERT: o 151 LYS cc_start: 0.7011 (mmtp) cc_final: 0.6802 (mptp) REVERT: o 186 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7169 (mtm-85) REVERT: o 193 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7300 (ttt90) REVERT: o 274 ASP cc_start: 0.6395 (t0) cc_final: 0.6091 (t0) REVERT: o 316 THR cc_start: 0.6743 (m) cc_final: 0.6390 (p) REVERT: o 321 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7402 (mt-10) REVERT: o 347 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7278 (mm-30) REVERT: o 439 HIS cc_start: 0.6497 (t-90) cc_final: 0.5919 (t-90) REVERT: o 486 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7320 (mt) REVERT: o 524 MET cc_start: 0.8359 (mmp) cc_final: 0.7646 (mmm) REVERT: o 556 GLU cc_start: 0.6355 (pt0) cc_final: 0.5872 (tp30) REVERT: o 612 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6739 (p0) REVERT: o 700 GLN cc_start: 0.6579 (tt0) cc_final: 0.6081 (tp-100) REVERT: o 711 GLN cc_start: 0.6474 (tt0) cc_final: 0.6226 (mm-40) REVERT: o 726 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7728 (mp0) REVERT: o 803 LYS cc_start: 0.7749 (tttp) cc_final: 0.7456 (tptp) REVERT: o 818 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7652 (mp0) REVERT: o 845 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6257 (tt0) REVERT: o 861 GLN cc_start: 0.6770 (tp40) cc_final: 0.6121 (mt0) REVERT: o 919 LYS cc_start: 0.6803 (mttt) cc_final: 0.6471 (mmtm) REVERT: o 936 GLU cc_start: 0.6921 (tt0) cc_final: 0.6631 (tp30) REVERT: o 960 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6150 (ttm-80) REVERT: o 1133 LYS cc_start: 0.7485 (mttp) cc_final: 0.7195 (ptpp) REVERT: o 1146 GLN cc_start: 0.7766 (pp30) cc_final: 0.6730 (pp30) REVERT: o 1153 ARG cc_start: 0.6996 (mmm-85) cc_final: 0.6752 (mmm-85) REVERT: o 1167 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7163 (ttm-80) REVERT: o 1168 LYS cc_start: 0.7881 (mttt) cc_final: 0.7466 (mtpt) REVERT: o 1279 MET cc_start: 0.6735 (mtm) cc_final: 0.6381 (tpp) REVERT: o 1286 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6551 (mtp85) REVERT: o 1306 LYS cc_start: 0.6075 (mttt) cc_final: 0.5745 (mtpt) REVERT: o 1310 HIS cc_start: 0.6437 (p-80) cc_final: 0.6142 (p90) REVERT: o 1325 ASP cc_start: 0.7369 (m-30) cc_final: 0.7161 (m-30) REVERT: o 1337 GLU cc_start: 0.6374 (mt-10) cc_final: 0.6115 (mm-30) REVERT: o 1376 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5683 (ttmm) REVERT: o 1396 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5063 (mtp85) REVERT: o 1412 MET cc_start: 0.7700 (ttp) cc_final: 0.7348 (tmm) REVERT: o 1422 GLN cc_start: 0.6308 (mt0) cc_final: 0.5798 (mm110) REVERT: o 1452 LYS cc_start: 0.7540 (mttt) cc_final: 0.6743 (mmtm) REVERT: o 1484 MET cc_start: 0.2871 (ppp) cc_final: 0.2664 (ppp) REVERT: p 16 GLU cc_start: 0.5915 (mm-30) cc_final: 0.5685 (tp30) REVERT: p 53 MET cc_start: 0.6577 (mmm) cc_final: 0.6307 (mmm) REVERT: p 87 LYS cc_start: 0.7114 (tttt) cc_final: 0.6541 (tptt) REVERT: p 145 GLN cc_start: 0.7005 (mp-120) cc_final: 0.6671 (mp10) REVERT: p 152 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7367 (mm) REVERT: p 160 TYR cc_start: 0.7114 (m-80) cc_final: 0.6811 (m-80) REVERT: p 215 TYR cc_start: 0.6959 (m-80) cc_final: 0.6054 (m-80) REVERT: p 239 MET cc_start: 0.7113 (ttm) cc_final: 0.6714 (ttp) REVERT: p 298 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6594 (mtp) REVERT: p 313 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6967 (tm-30) REVERT: p 346 GLU cc_start: 0.6395 (mm-30) cc_final: 0.5981 (mm-30) REVERT: p 381 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7724 (mp0) REVERT: p 388 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: p 420 GLN cc_start: 0.6256 (tt0) cc_final: 0.5849 (tp40) REVERT: p 438 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5263 (ttp-110) REVERT: p 497 LYS cc_start: 0.7277 (tptp) cc_final: 0.6981 (tptt) REVERT: p 555 GLU cc_start: 0.7052 (pm20) cc_final: 0.6562 (tp30) REVERT: p 597 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7819 (mp) REVERT: p 617 ASP cc_start: 0.7008 (p0) cc_final: 0.6782 (p0) REVERT: p 728 MET cc_start: 0.7360 (mtm) cc_final: 0.6949 (mtp) REVERT: p 733 MET cc_start: 0.8192 (ttm) cc_final: 0.7940 (ttm) REVERT: p 761 THR cc_start: 0.7912 (m) cc_final: 0.7566 (p) REVERT: p 771 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: p 796 MET cc_start: 0.8858 (mtm) cc_final: 0.8602 (mtm) REVERT: p 817 GLN cc_start: 0.8013 (pt0) cc_final: 0.7725 (pt0) REVERT: p 846 ASP cc_start: 0.8449 (m-30) cc_final: 0.8107 (p0) REVERT: p 850 ASP cc_start: 0.8136 (t0) cc_final: 0.7854 (p0) REVERT: p 1041 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (mp) REVERT: p 1091 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.4808 (ptt-90) REVERT: p 1151 MET cc_start: 0.7773 (ptm) cc_final: 0.7566 (ptm) REVERT: p 1172 MET cc_start: 0.7491 (mmt) cc_final: 0.7188 (mmt) REVERT: q 17 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7222 (pt0) REVERT: q 24 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6777 (mt-10) REVERT: q 109 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6304 (pm20) REVERT: q 111 GLN cc_start: 0.8230 (tt0) cc_final: 0.7788 (mp10) REVERT: q 126 ARG cc_start: 0.7456 (mtt180) cc_final: 0.7020 (mmm-85) REVERT: q 158 GLU cc_start: 0.7139 (tt0) cc_final: 0.6322 (tt0) REVERT: q 253 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6497 (ttmt) REVERT: q 265 HIS cc_start: 0.7503 (t70) cc_final: 0.6493 (t-170) REVERT: q 268 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6748 (tm-30) REVERT: s 49 SER cc_start: 0.8299 (t) cc_final: 0.7988 (p) REVERT: s 120 ASP cc_start: 0.6954 (m-30) cc_final: 0.6709 (m-30) REVERT: s 133 GLN cc_start: 0.7939 (mt0) cc_final: 0.7446 (tp-100) REVERT: s 137 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6814 (pp) REVERT: s 159 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6205 (tp) REVERT: t 79 VAL cc_start: 0.6773 (t) cc_final: 0.6145 (t) REVERT: t 81 VAL cc_start: 0.6592 (t) cc_final: 0.5971 (m) REVERT: t 86 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6455 (mm-30) REVERT: t 91 LEU cc_start: 0.6681 (mt) cc_final: 0.6463 (mt) REVERT: u 104 MET cc_start: 0.5594 (tpp) cc_final: 0.4759 (tpt) REVERT: u 156 ASP cc_start: 0.8733 (t0) cc_final: 0.7705 (m-30) REVERT: u 165 ASP cc_start: 0.7571 (m-30) cc_final: 0.7358 (t0) REVERT: v 4 ILE cc_start: 0.8273 (mt) cc_final: 0.8048 (mm) REVERT: v 46 GLN cc_start: 0.7906 (mt0) cc_final: 0.7441 (tt0) REVERT: v 63 THR cc_start: 0.8996 (p) cc_final: 0.8630 (t) REVERT: v 71 ASP cc_start: 0.6497 (m-30) cc_final: 0.6043 (m-30) REVERT: v 74 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: v 79 ASP cc_start: 0.5737 (m-30) cc_final: 0.5335 (t70) REVERT: v 95 LYS cc_start: 0.7177 (tttt) cc_final: 0.6733 (ttpt) REVERT: v 100 GLU cc_start: 0.7754 (tt0) cc_final: 0.6835 (mt-10) REVERT: v 123 MET cc_start: 0.8102 (ttt) cc_final: 0.7872 (ttp) REVERT: v 133 HIS cc_start: 0.7311 (p-80) cc_final: 0.6830 (m170) REVERT: w 18 GLN cc_start: 0.8419 (mt0) cc_final: 0.7840 (pp30) REVERT: w 27 LYS cc_start: 0.7378 (ttpp) cc_final: 0.6640 (ttpp) REVERT: w 47 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: w 51 SER cc_start: 0.6421 (t) cc_final: 0.6220 (p) REVERT: w 68 ILE cc_start: 0.7592 (mt) cc_final: 0.7335 (mm) REVERT: w 69 ILE cc_start: 0.8122 (mt) cc_final: 0.7699 (mp) REVERT: w 71 ASP cc_start: 0.6905 (m-30) cc_final: 0.6642 (m-30) REVERT: w 93 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6483 (mm-30) REVERT: w 115 THR cc_start: 0.6018 (m) cc_final: 0.5454 (p) REVERT: x 19 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: x 57 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8032 (mm-30) REVERT: y 23 LYS cc_start: 0.8203 (mttt) cc_final: 0.7617 (mptm) REVERT: y 55 GLN cc_start: 0.7696 (mt0) cc_final: 0.7394 (mt0) REVERT: y 70 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7470 (ttmm) REVERT: y 93 ASP cc_start: 0.7225 (m-30) cc_final: 0.6850 (m-30) REVERT: z 18 ILE cc_start: 0.7948 (mt) cc_final: 0.7743 (mm) REVERT: z 25 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6808 (mp0) REVERT: z 35 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7619 (mtp85) REVERT: z 56 ASP cc_start: 0.7482 (m-30) cc_final: 0.7154 (p0) outliers start: 161 outliers final: 79 residues processed: 654 average time/residue: 1.6399 time to fit residues: 1270.1667 Evaluate side-chains 635 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 535 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 407 ARG Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 486 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 852 VAL Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1031 ARG Chi-restraints excluded: chain o residue 1050 CYS Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 169 ARG Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 224 CYS Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 266 GLU Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 89 THR Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 253 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 137 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 110 THR Chi-restraints excluded: chain v residue 145 MET Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 5 VAL Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 407 optimal weight: 2.9990 chunk 338 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 213 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 265 GLN p 344 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 631 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 825 GLN p 948 GLN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 66 HIS q 83 GLN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 GLN s 168 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5443 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36619 Z= 0.182 Angle : 0.455 9.778 49945 Z= 0.244 Chirality : 0.039 0.169 5562 Planarity : 0.003 0.047 6098 Dihedral : 16.241 144.113 5824 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 3.31 % Allowed : 19.17 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.58 (0.13), residues: 4137 helix: 1.69 (0.14), residues: 1405 sheet: -0.13 (0.19), residues: 679 loop : -0.30 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 679 HIS 0.005 0.001 HIS o 84 PHE 0.017 0.001 PHE o 234 TYR 0.017 0.001 TYR u 167 ARG 0.007 0.000 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 543 time to evaluate : 3.216 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: o 16 ARG cc_start: 0.6965 (mmt90) cc_final: 0.6494 (mtt-85) REVERT: o 18 ILE cc_start: 0.8570 (mt) cc_final: 0.8233 (mm) REVERT: o 30 GLU cc_start: 0.6620 (tt0) cc_final: 0.6222 (tt0) REVERT: o 58 MET cc_start: 0.7743 (ttp) cc_final: 0.7328 (ttp) REVERT: o 115 SER cc_start: 0.7186 (p) cc_final: 0.6796 (t) REVERT: o 193 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7390 (ttt90) REVERT: o 223 GLU cc_start: 0.7727 (tp30) cc_final: 0.7392 (tp30) REVERT: o 246 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6501 (pt0) REVERT: o 274 ASP cc_start: 0.6364 (t0) cc_final: 0.5551 (t70) REVERT: o 294 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6162 (mt-10) REVERT: o 316 THR cc_start: 0.6807 (m) cc_final: 0.6509 (p) REVERT: o 321 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7042 (mp0) REVERT: o 347 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7236 (mm-30) REVERT: o 439 HIS cc_start: 0.6532 (t-90) cc_final: 0.5964 (t-90) REVERT: o 524 MET cc_start: 0.8270 (mmp) cc_final: 0.7694 (mmm) REVERT: o 556 GLU cc_start: 0.6336 (pt0) cc_final: 0.5899 (tp30) REVERT: o 612 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6746 (p0) REVERT: o 700 GLN cc_start: 0.6515 (tt0) cc_final: 0.5975 (tp-100) REVERT: o 711 GLN cc_start: 0.6392 (tt0) cc_final: 0.6152 (mm-40) REVERT: o 726 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7683 (mp0) REVERT: o 803 LYS cc_start: 0.7787 (tttp) cc_final: 0.7484 (tptp) REVERT: o 818 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7450 (mp0) REVERT: o 857 THR cc_start: 0.6842 (p) cc_final: 0.6585 (m) REVERT: o 861 GLN cc_start: 0.6923 (tp40) cc_final: 0.6248 (mt0) REVERT: o 919 LYS cc_start: 0.6687 (mttt) cc_final: 0.6420 (mmtm) REVERT: o 1133 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (ptpp) REVERT: o 1146 GLN cc_start: 0.7793 (pp30) cc_final: 0.6785 (pp30) REVERT: o 1153 ARG cc_start: 0.7040 (mmm-85) cc_final: 0.6833 (mmm-85) REVERT: o 1262 MET cc_start: 0.6087 (tpp) cc_final: 0.5752 (tpt) REVERT: o 1279 MET cc_start: 0.6717 (mtm) cc_final: 0.6367 (tpp) REVERT: o 1286 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6566 (mtp85) REVERT: o 1306 LYS cc_start: 0.5991 (mttt) cc_final: 0.5689 (mtpt) REVERT: o 1310 HIS cc_start: 0.6397 (p-80) cc_final: 0.6088 (p90) REVERT: o 1337 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6095 (mm-30) REVERT: o 1376 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5672 (ttmm) REVERT: o 1412 MET cc_start: 0.7641 (ttp) cc_final: 0.7170 (tmm) REVERT: o 1422 GLN cc_start: 0.6298 (mt0) cc_final: 0.5768 (mm110) REVERT: o 1452 LYS cc_start: 0.7499 (mttt) cc_final: 0.6744 (mmtm) REVERT: p 16 GLU cc_start: 0.5905 (mm-30) cc_final: 0.5684 (tp30) REVERT: p 53 MET cc_start: 0.6733 (mmm) cc_final: 0.6143 (mmm) REVERT: p 87 LYS cc_start: 0.7069 (tttt) cc_final: 0.6503 (tptt) REVERT: p 91 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6784 (tp) REVERT: p 145 GLN cc_start: 0.7148 (mp-120) cc_final: 0.6763 (mp10) REVERT: p 152 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7324 (mm) REVERT: p 215 TYR cc_start: 0.6883 (m-80) cc_final: 0.5981 (m-80) REVERT: p 239 MET cc_start: 0.7036 (ttm) cc_final: 0.6635 (ttp) REVERT: p 298 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: p 313 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6934 (tm-30) REVERT: p 346 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6031 (mm-30) REVERT: p 381 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7775 (mp0) REVERT: p 388 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: p 420 GLN cc_start: 0.6166 (tt0) cc_final: 0.5783 (tp40) REVERT: p 438 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5262 (ttp-110) REVERT: p 555 GLU cc_start: 0.6966 (pm20) cc_final: 0.6510 (tp30) REVERT: p 561 ILE cc_start: 0.5767 (OUTLIER) cc_final: 0.5565 (mt) REVERT: p 597 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7806 (mp) REVERT: p 637 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7364 (ttmm) REVERT: p 728 MET cc_start: 0.7287 (mtm) cc_final: 0.6964 (mtp) REVERT: p 761 THR cc_start: 0.7774 (m) cc_final: 0.7418 (p) REVERT: p 771 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: p 796 MET cc_start: 0.8850 (mtm) cc_final: 0.8592 (mtm) REVERT: p 817 GLN cc_start: 0.8012 (pt0) cc_final: 0.7723 (pt0) REVERT: p 846 ASP cc_start: 0.8366 (m-30) cc_final: 0.8069 (p0) REVERT: p 850 ASP cc_start: 0.8127 (t0) cc_final: 0.7844 (p0) REVERT: p 863 ASP cc_start: 0.7066 (t0) cc_final: 0.6654 (m-30) REVERT: p 890 ARG cc_start: 0.5987 (ttt180) cc_final: 0.5754 (ttp-170) REVERT: p 1151 MET cc_start: 0.7735 (ptm) cc_final: 0.7292 (ptm) REVERT: q 17 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7177 (pt0) REVERT: q 24 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6652 (mt-10) REVERT: q 109 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6258 (pm20) REVERT: q 111 GLN cc_start: 0.8374 (tt0) cc_final: 0.7814 (mp10) REVERT: q 158 GLU cc_start: 0.7150 (tt0) cc_final: 0.6492 (pt0) REVERT: q 265 HIS cc_start: 0.7363 (t70) cc_final: 0.6446 (t-170) REVERT: q 268 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6755 (tm-30) REVERT: s 4 GLU cc_start: 0.6837 (pm20) cc_final: 0.6127 (pm20) REVERT: s 49 SER cc_start: 0.8306 (t) cc_final: 0.7955 (p) REVERT: s 96 GLU cc_start: 0.8792 (tp30) cc_final: 0.8534 (tm-30) REVERT: s 120 ASP cc_start: 0.6760 (m-30) cc_final: 0.6518 (m-30) REVERT: s 133 GLN cc_start: 0.7922 (mt0) cc_final: 0.7402 (tp-100) REVERT: t 79 VAL cc_start: 0.6891 (t) cc_final: 0.6311 (t) REVERT: t 81 VAL cc_start: 0.6545 (t) cc_final: 0.5931 (m) REVERT: t 86 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6088 (mm-30) REVERT: t 88 ASP cc_start: 0.6898 (t0) cc_final: 0.6574 (t0) REVERT: t 91 LEU cc_start: 0.6751 (mt) cc_final: 0.6417 (mt) REVERT: u 166 ASP cc_start: 0.9076 (p0) cc_final: 0.8794 (p0) REVERT: v 4 ILE cc_start: 0.8268 (mt) cc_final: 0.8049 (mm) REVERT: v 46 GLN cc_start: 0.7897 (mt0) cc_final: 0.7429 (tt0) REVERT: v 71 ASP cc_start: 0.6739 (m-30) cc_final: 0.6317 (m-30) REVERT: v 74 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: v 95 LYS cc_start: 0.7087 (tttt) cc_final: 0.6694 (ttpt) REVERT: v 100 GLU cc_start: 0.7991 (tt0) cc_final: 0.6949 (mt-10) REVERT: v 133 HIS cc_start: 0.7289 (p-80) cc_final: 0.6794 (m170) REVERT: w 18 GLN cc_start: 0.8409 (mt0) cc_final: 0.7805 (pp30) REVERT: w 27 LYS cc_start: 0.7333 (ttpp) cc_final: 0.6622 (ttpp) REVERT: w 47 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: w 51 SER cc_start: 0.6482 (t) cc_final: 0.6264 (p) REVERT: w 68 ILE cc_start: 0.7516 (mt) cc_final: 0.7251 (mm) REVERT: w 71 ASP cc_start: 0.6936 (m-30) cc_final: 0.6663 (m-30) REVERT: w 93 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6374 (mm-30) REVERT: w 115 THR cc_start: 0.6027 (m) cc_final: 0.5339 (p) REVERT: y 23 LYS cc_start: 0.8208 (mttt) cc_final: 0.7633 (mptm) REVERT: y 55 GLN cc_start: 0.7601 (mt0) cc_final: 0.7233 (mt0) REVERT: y 70 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7246 (ttmm) REVERT: y 93 ASP cc_start: 0.7187 (m-30) cc_final: 0.6852 (m-30) REVERT: z 25 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7088 (mp0) REVERT: z 35 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7617 (mtp85) REVERT: z 56 ASP cc_start: 0.7479 (m-30) cc_final: 0.7143 (p0) outliers start: 122 outliers final: 68 residues processed: 617 average time/residue: 1.6499 time to fit residues: 1209.8415 Evaluate side-chains 610 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 527 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1050 CYS Chi-restraints excluded: chain o residue 1063 GLU Chi-restraints excluded: chain o residue 1075 LYS Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 224 CYS Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 145 MET Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1163 HIS ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 111 ASN p 265 GLN p 312 GLN p 456 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 948 GLN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 66 HIS q 83 GLN ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN v 76 ASN x 16 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 36619 Z= 0.383 Angle : 0.546 10.303 49945 Z= 0.287 Chirality : 0.043 0.174 5562 Planarity : 0.004 0.059 6098 Dihedral : 16.262 147.517 5824 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.98 % Favored : 94.83 % Rotamer: Outliers : 3.88 % Allowed : 19.14 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 4137 helix: 1.47 (0.14), residues: 1395 sheet: -0.22 (0.19), residues: 681 loop : -0.42 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 49 HIS 0.007 0.001 HIS o 84 PHE 0.019 0.002 PHE q 63 TYR 0.021 0.002 TYR p 160 ARG 0.013 0.001 ARG o 931 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 535 time to evaluate : 4.030 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: o 16 ARG cc_start: 0.6977 (mmt90) cc_final: 0.6452 (mtt-85) REVERT: o 18 ILE cc_start: 0.8597 (mt) cc_final: 0.8286 (mm) REVERT: o 30 GLU cc_start: 0.6607 (tt0) cc_final: 0.6225 (tt0) REVERT: o 58 MET cc_start: 0.7918 (ttp) cc_final: 0.7591 (ttp) REVERT: o 115 SER cc_start: 0.7072 (p) cc_final: 0.6718 (t) REVERT: o 193 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7244 (ttt180) REVERT: o 223 GLU cc_start: 0.7754 (tp30) cc_final: 0.7379 (tp30) REVERT: o 274 ASP cc_start: 0.6379 (t0) cc_final: 0.5577 (t70) REVERT: o 316 THR cc_start: 0.6724 (m) cc_final: 0.6397 (p) REVERT: o 321 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7023 (mp0) REVERT: o 347 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7241 (mm-30) REVERT: o 439 HIS cc_start: 0.6606 (t-90) cc_final: 0.5914 (t-90) REVERT: o 486 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7231 (mt) REVERT: o 524 MET cc_start: 0.8338 (mmp) cc_final: 0.7660 (mmm) REVERT: o 556 GLU cc_start: 0.6457 (pt0) cc_final: 0.5928 (tp30) REVERT: o 612 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6753 (p0) REVERT: o 700 GLN cc_start: 0.6565 (tt0) cc_final: 0.6070 (tp-100) REVERT: o 711 GLN cc_start: 0.6396 (tt0) cc_final: 0.6163 (mm-40) REVERT: o 726 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7711 (mp0) REVERT: o 803 LYS cc_start: 0.7768 (tttp) cc_final: 0.7459 (tptp) REVERT: o 818 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7663 (mp0) REVERT: o 861 GLN cc_start: 0.6755 (tp40) cc_final: 0.6111 (mt0) REVERT: o 919 LYS cc_start: 0.6763 (mttt) cc_final: 0.6547 (mmtp) REVERT: o 1133 LYS cc_start: 0.7511 (mttp) cc_final: 0.7257 (ptpp) REVERT: o 1146 GLN cc_start: 0.7828 (pp30) cc_final: 0.6733 (tp-100) REVERT: o 1153 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6578 (mmm-85) REVERT: o 1167 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7252 (ttm-80) REVERT: o 1279 MET cc_start: 0.6741 (mtm) cc_final: 0.6392 (tpp) REVERT: o 1286 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6545 (mtp85) REVERT: o 1306 LYS cc_start: 0.6033 (mttt) cc_final: 0.5733 (mtpt) REVERT: o 1376 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.5690 (ttmm) REVERT: o 1396 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5082 (mtp85) REVERT: o 1412 MET cc_start: 0.7668 (ttp) cc_final: 0.7203 (tmm) REVERT: o 1422 GLN cc_start: 0.6366 (mt0) cc_final: 0.5763 (mm110) REVERT: o 1452 LYS cc_start: 0.7268 (mttt) cc_final: 0.6647 (mmtm) REVERT: p 16 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5649 (tp30) REVERT: p 53 MET cc_start: 0.6373 (mmm) cc_final: 0.5947 (mmm) REVERT: p 87 LYS cc_start: 0.7147 (tttt) cc_final: 0.6583 (tptt) REVERT: p 145 GLN cc_start: 0.7107 (mp-120) cc_final: 0.6733 (mp10) REVERT: p 152 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7373 (mm) REVERT: p 239 MET cc_start: 0.7099 (ttm) cc_final: 0.6748 (ttp) REVERT: p 298 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6431 (mtp) REVERT: p 313 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7017 (tm-30) REVERT: p 346 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6025 (mm-30) REVERT: p 381 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7765 (mp0) REVERT: p 388 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: p 420 GLN cc_start: 0.6238 (tt0) cc_final: 0.5841 (tp40) REVERT: p 438 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5313 (ttp-110) REVERT: p 528 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7981 (mt) REVERT: p 555 GLU cc_start: 0.7127 (pm20) cc_final: 0.6599 (tp30) REVERT: p 597 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7847 (mp) REVERT: p 617 ASP cc_start: 0.7159 (p0) cc_final: 0.6902 (p0) REVERT: p 629 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6949 (mt-10) REVERT: p 637 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7418 (ttmm) REVERT: p 728 MET cc_start: 0.7427 (mtm) cc_final: 0.7064 (mtp) REVERT: p 761 THR cc_start: 0.7851 (m) cc_final: 0.7475 (p) REVERT: p 771 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: p 796 MET cc_start: 0.8866 (mtm) cc_final: 0.8637 (mtm) REVERT: p 817 GLN cc_start: 0.8034 (pt0) cc_final: 0.7745 (pt0) REVERT: p 846 ASP cc_start: 0.8469 (m-30) cc_final: 0.8113 (p0) REVERT: p 850 ASP cc_start: 0.8092 (t0) cc_final: 0.7824 (p0) REVERT: p 890 ARG cc_start: 0.5967 (ttt180) cc_final: 0.5735 (ttp-170) REVERT: p 942 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6842 (pttt) REVERT: p 1091 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4802 (ptt-90) REVERT: p 1151 MET cc_start: 0.7785 (ptm) cc_final: 0.7338 (ptm) REVERT: q 17 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7220 (pt0) REVERT: q 24 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6764 (mt-10) REVERT: q 106 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6737 (ttm170) REVERT: q 109 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6703 (pm20) REVERT: q 111 GLN cc_start: 0.8280 (tt0) cc_final: 0.7837 (mp10) REVERT: q 126 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7048 (mmm-85) REVERT: q 158 GLU cc_start: 0.7205 (tt0) cc_final: 0.6732 (pt0) REVERT: q 253 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6421 (ttmt) REVERT: q 265 HIS cc_start: 0.7330 (t70) cc_final: 0.6367 (t-170) REVERT: q 268 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6837 (tm-30) REVERT: s 49 SER cc_start: 0.8439 (t) cc_final: 0.8151 (p) REVERT: s 85 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7532 (mmmt) REVERT: s 120 ASP cc_start: 0.6814 (m-30) cc_final: 0.6559 (m-30) REVERT: s 133 GLN cc_start: 0.7772 (mt0) cc_final: 0.7276 (tp-100) REVERT: t 79 VAL cc_start: 0.6738 (t) cc_final: 0.6482 (t) REVERT: t 81 VAL cc_start: 0.6597 (t) cc_final: 0.6127 (m) REVERT: t 86 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6593 (mm-30) REVERT: t 122 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6901 (mt-10) REVERT: u 104 MET cc_start: 0.5808 (tpp) cc_final: 0.4919 (tpt) REVERT: v 4 ILE cc_start: 0.8269 (mt) cc_final: 0.8046 (mm) REVERT: v 46 GLN cc_start: 0.7897 (mt0) cc_final: 0.7405 (tt0) REVERT: v 74 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: v 95 LYS cc_start: 0.7148 (tttt) cc_final: 0.6717 (ttpt) REVERT: v 100 GLU cc_start: 0.7892 (tt0) cc_final: 0.6915 (mt-10) REVERT: v 133 HIS cc_start: 0.7302 (p-80) cc_final: 0.6815 (m170) REVERT: w 18 GLN cc_start: 0.8443 (mt0) cc_final: 0.7885 (pp30) REVERT: w 25 TYR cc_start: 0.7297 (m-80) cc_final: 0.6948 (m-10) REVERT: w 27 LYS cc_start: 0.7458 (ttpp) cc_final: 0.6701 (ttpp) REVERT: w 47 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: w 51 SER cc_start: 0.6448 (t) cc_final: 0.6229 (p) REVERT: w 68 ILE cc_start: 0.7503 (mt) cc_final: 0.7212 (mm) REVERT: w 71 ASP cc_start: 0.6922 (m-30) cc_final: 0.6667 (m-30) REVERT: w 93 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6530 (mm-30) REVERT: w 115 THR cc_start: 0.6013 (m) cc_final: 0.5448 (p) REVERT: x 19 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: y 23 LYS cc_start: 0.8161 (mttt) cc_final: 0.7539 (mptm) REVERT: y 55 GLN cc_start: 0.7730 (mt0) cc_final: 0.7435 (mt0) REVERT: y 70 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7232 (ttmt) REVERT: y 93 ASP cc_start: 0.7180 (m-30) cc_final: 0.6808 (m-30) REVERT: z 25 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7124 (mp0) REVERT: z 35 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7613 (mtp85) REVERT: z 56 ASP cc_start: 0.7521 (m-30) cc_final: 0.7146 (p0) outliers start: 143 outliers final: 87 residues processed: 627 average time/residue: 1.6670 time to fit residues: 1239.9922 Evaluate side-chains 630 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 523 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 486 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 852 VAL Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1031 ARG Chi-restraints excluded: chain o residue 1050 CYS Chi-restraints excluded: chain o residue 1063 GLU Chi-restraints excluded: chain o residue 1075 LYS Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 159 THR Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 224 CYS Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 763 SER Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 89 THR Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 253 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 141 ASP Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 55 LEU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 52 LEU Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 0.9990 chunk 162 optimal weight: 0.0060 chunk 242 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 276 optimal weight: 0.0770 chunk 200 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 318 optimal weight: 40.0000 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1163 HIS o1220 HIS o1310 HIS p 265 GLN p 344 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 948 GLN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 66 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 30 GLN s 168 ASN v 76 ASN w 41 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36619 Z= 0.147 Angle : 0.434 9.778 49945 Z= 0.233 Chirality : 0.038 0.177 5562 Planarity : 0.003 0.052 6098 Dihedral : 16.070 153.491 5824 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 2.47 % Allowed : 20.91 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.72 (0.13), residues: 4137 helix: 1.92 (0.14), residues: 1398 sheet: -0.11 (0.19), residues: 675 loop : -0.27 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 679 HIS 0.005 0.001 HIS o 84 PHE 0.016 0.001 PHE o 234 TYR 0.015 0.001 TYR t 115 ARG 0.008 0.000 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 536 time to evaluate : 3.475 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: o 16 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6424 (mtt-85) REVERT: o 18 ILE cc_start: 0.8588 (mt) cc_final: 0.8220 (mm) REVERT: o 30 GLU cc_start: 0.6613 (tt0) cc_final: 0.6229 (tt0) REVERT: o 38 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7577 (mm-30) REVERT: o 58 MET cc_start: 0.7746 (ttp) cc_final: 0.7372 (ttp) REVERT: o 115 SER cc_start: 0.7105 (p) cc_final: 0.6773 (t) REVERT: o 186 ARG cc_start: 0.7015 (mtt90) cc_final: 0.6442 (mtm-85) REVERT: o 193 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7231 (ttt180) REVERT: o 197 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7070 (mt-10) REVERT: o 223 GLU cc_start: 0.7728 (tp30) cc_final: 0.7376 (tp30) REVERT: o 246 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: o 274 ASP cc_start: 0.6331 (t0) cc_final: 0.5537 (t70) REVERT: o 294 GLU cc_start: 0.6385 (tm-30) cc_final: 0.6166 (mt-10) REVERT: o 316 THR cc_start: 0.6767 (m) cc_final: 0.6503 (p) REVERT: o 321 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7064 (mp0) REVERT: o 322 LEU cc_start: 0.6661 (mt) cc_final: 0.6380 (mt) REVERT: o 347 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7238 (mm-30) REVERT: o 524 MET cc_start: 0.8215 (mmp) cc_final: 0.7664 (mmm) REVERT: o 556 GLU cc_start: 0.6394 (pt0) cc_final: 0.5826 (tp30) REVERT: o 612 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6753 (p0) REVERT: o 700 GLN cc_start: 0.6493 (tt0) cc_final: 0.5914 (tp-100) REVERT: o 711 GLN cc_start: 0.6353 (tt0) cc_final: 0.6147 (mm-40) REVERT: o 726 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7676 (mp0) REVERT: o 803 LYS cc_start: 0.7846 (tttp) cc_final: 0.7452 (tptp) REVERT: o 818 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7695 (mp0) REVERT: o 857 THR cc_start: 0.6743 (p) cc_final: 0.6379 (m) REVERT: o 861 GLN cc_start: 0.6866 (tp40) cc_final: 0.6190 (mt0) REVERT: o 917 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: o 919 LYS cc_start: 0.6739 (mttt) cc_final: 0.6472 (mmtp) REVERT: o 1133 LYS cc_start: 0.7537 (mttp) cc_final: 0.7324 (ptpp) REVERT: o 1146 GLN cc_start: 0.7830 (pp30) cc_final: 0.6724 (tp-100) REVERT: o 1153 ARG cc_start: 0.6977 (mmm-85) cc_final: 0.6544 (mmm-85) REVERT: o 1167 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7165 (ttm-80) REVERT: o 1279 MET cc_start: 0.6798 (mtm) cc_final: 0.6449 (tpp) REVERT: o 1286 ARG cc_start: 0.6856 (mtp85) cc_final: 0.6427 (mtp85) REVERT: o 1306 LYS cc_start: 0.5984 (mttt) cc_final: 0.5645 (mtpt) REVERT: o 1376 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5646 (ttmm) REVERT: o 1412 MET cc_start: 0.7607 (ttp) cc_final: 0.7157 (tmm) REVERT: o 1422 GLN cc_start: 0.6361 (mt0) cc_final: 0.5749 (mm110) REVERT: o 1437 ASP cc_start: 0.7369 (m-30) cc_final: 0.6818 (m-30) REVERT: o 1451 MET cc_start: 0.8160 (mmm) cc_final: 0.7894 (mmm) REVERT: o 1452 LYS cc_start: 0.7191 (mttt) cc_final: 0.6614 (mmtm) REVERT: p 53 MET cc_start: 0.6644 (mmm) cc_final: 0.6092 (mmm) REVERT: p 87 LYS cc_start: 0.6741 (tttt) cc_final: 0.6179 (tptt) REVERT: p 239 MET cc_start: 0.7018 (ttm) cc_final: 0.6640 (ttp) REVERT: p 298 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6343 (mtp) REVERT: p 313 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6929 (tm-30) REVERT: p 345 LYS cc_start: 0.6753 (mptt) cc_final: 0.6487 (mmtm) REVERT: p 346 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6048 (mm-30) REVERT: p 381 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7768 (mp0) REVERT: p 388 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: p 420 GLN cc_start: 0.6037 (tt0) cc_final: 0.5647 (tp40) REVERT: p 438 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5435 (ttp-110) REVERT: p 555 GLU cc_start: 0.7184 (pm20) cc_final: 0.6642 (tp30) REVERT: p 578 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7507 (mptt) REVERT: p 597 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7829 (mp) REVERT: p 629 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6988 (mt-10) REVERT: p 691 SER cc_start: 0.8239 (p) cc_final: 0.7797 (t) REVERT: p 728 MET cc_start: 0.7202 (mtm) cc_final: 0.6853 (mtp) REVERT: p 761 THR cc_start: 0.7721 (m) cc_final: 0.7447 (p) REVERT: p 796 MET cc_start: 0.8853 (mtm) cc_final: 0.8595 (mtm) REVERT: p 817 GLN cc_start: 0.8031 (pt0) cc_final: 0.7731 (pt0) REVERT: p 846 ASP cc_start: 0.8379 (m-30) cc_final: 0.8077 (p0) REVERT: p 850 ASP cc_start: 0.8082 (t0) cc_final: 0.7823 (p0) REVERT: p 863 ASP cc_start: 0.7235 (t0) cc_final: 0.6893 (t0) REVERT: p 896 LEU cc_start: 0.7870 (tp) cc_final: 0.7414 (tt) REVERT: p 1054 MET cc_start: 0.8326 (mtt) cc_final: 0.7878 (mtt) REVERT: p 1151 MET cc_start: 0.7729 (ptm) cc_final: 0.7280 (ptm) REVERT: q 17 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7215 (pt0) REVERT: q 24 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6675 (mt-10) REVERT: q 109 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6231 (pm20) REVERT: q 110 ASP cc_start: 0.8050 (t0) cc_final: 0.7627 (m-30) REVERT: q 111 GLN cc_start: 0.8379 (tt0) cc_final: 0.7905 (mp10) REVERT: q 158 GLU cc_start: 0.7167 (tt0) cc_final: 0.6506 (pt0) REVERT: q 225 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7709 (ptmm) REVERT: q 253 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6397 (ttmt) REVERT: q 265 HIS cc_start: 0.7221 (t70) cc_final: 0.6322 (t-170) REVERT: q 268 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6764 (tm-30) REVERT: s 49 SER cc_start: 0.8424 (t) cc_final: 0.8133 (p) REVERT: s 85 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7496 (mmmt) REVERT: s 120 ASP cc_start: 0.6741 (m-30) cc_final: 0.6463 (m-30) REVERT: s 133 GLN cc_start: 0.7719 (mt0) cc_final: 0.7199 (tp-100) REVERT: t 81 VAL cc_start: 0.6453 (t) cc_final: 0.6095 (m) REVERT: t 86 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6581 (mm-30) REVERT: t 110 LEU cc_start: 0.7196 (mt) cc_final: 0.6894 (mt) REVERT: t 122 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6890 (mt-10) REVERT: u 104 MET cc_start: 0.5841 (tpp) cc_final: 0.5002 (tpt) REVERT: u 165 ASP cc_start: 0.6740 (t0) cc_final: 0.6518 (t0) REVERT: v 4 ILE cc_start: 0.8300 (mt) cc_final: 0.8093 (mm) REVERT: v 37 MET cc_start: 0.7615 (mtp) cc_final: 0.7099 (mtm) REVERT: v 46 GLN cc_start: 0.7898 (mt0) cc_final: 0.7409 (tt0) REVERT: v 95 LYS cc_start: 0.7056 (tttt) cc_final: 0.6671 (ttpt) REVERT: v 100 GLU cc_start: 0.7986 (tt0) cc_final: 0.6923 (mt-10) REVERT: v 133 HIS cc_start: 0.7268 (p-80) cc_final: 0.6769 (m170) REVERT: w 18 GLN cc_start: 0.8414 (mt0) cc_final: 0.7953 (tm-30) REVERT: w 27 LYS cc_start: 0.7425 (ttpp) cc_final: 0.6808 (ttpp) REVERT: w 44 TYR cc_start: 0.6920 (t80) cc_final: 0.6685 (t80) REVERT: w 47 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: w 51 SER cc_start: 0.6551 (t) cc_final: 0.6333 (p) REVERT: w 68 ILE cc_start: 0.7655 (mt) cc_final: 0.7423 (mm) REVERT: w 71 ASP cc_start: 0.6961 (m-30) cc_final: 0.6687 (m-30) REVERT: w 93 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6310 (mm-30) REVERT: w 115 THR cc_start: 0.5967 (m) cc_final: 0.5317 (p) REVERT: y 23 LYS cc_start: 0.8202 (mttt) cc_final: 0.7651 (mptm) REVERT: y 55 GLN cc_start: 0.7684 (mt0) cc_final: 0.7265 (mt0) REVERT: y 70 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7055 (ttmt) REVERT: y 93 ASP cc_start: 0.7158 (m-30) cc_final: 0.6818 (m-30) REVERT: z 25 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7101 (mp0) REVERT: z 29 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7161 (mmpt) REVERT: z 35 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7404 (mtp85) REVERT: z 42 ARG cc_start: 0.7587 (mmt180) cc_final: 0.7350 (mtt180) REVERT: z 56 ASP cc_start: 0.7510 (m-30) cc_final: 0.7126 (p0) outliers start: 91 outliers final: 48 residues processed: 591 average time/residue: 1.6297 time to fit residues: 1140.0900 Evaluate side-chains 585 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 525 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 917 GLU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 253 LYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 47 GLU Chi-restraints excluded: chain x residue 5 VAL Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 29 LYS Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 20.0000 chunk 388 optimal weight: 3.9990 chunk 354 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 357 optimal weight: 0.8980 chunk 376 optimal weight: 0.0070 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 204 HIS o 301 HIS ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 265 GLN p 344 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 948 GLN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36619 Z= 0.229 Angle : 0.460 9.986 49945 Z= 0.244 Chirality : 0.040 0.168 5562 Planarity : 0.003 0.053 6098 Dihedral : 16.027 154.236 5823 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.45 % Favored : 95.38 % Rotamer: Outliers : 2.66 % Allowed : 21.10 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.73 (0.13), residues: 4137 helix: 1.91 (0.14), residues: 1399 sheet: -0.13 (0.19), residues: 677 loop : -0.24 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o1334 HIS 0.006 0.001 HIS o 84 PHE 0.017 0.001 PHE o 234 TYR 0.021 0.001 TYR w 25 ARG 0.009 0.000 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 531 time to evaluate : 4.328 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: o 16 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6418 (mtt-85) REVERT: o 18 ILE cc_start: 0.8606 (mt) cc_final: 0.8276 (mm) REVERT: o 30 GLU cc_start: 0.6599 (tt0) cc_final: 0.6212 (tt0) REVERT: o 38 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7617 (mm-30) REVERT: o 58 MET cc_start: 0.7750 (ttp) cc_final: 0.7393 (ttp) REVERT: o 115 SER cc_start: 0.7188 (p) cc_final: 0.6862 (t) REVERT: o 186 ARG cc_start: 0.7147 (mtt90) cc_final: 0.6915 (mtt90) REVERT: o 192 ARG cc_start: 0.7553 (ptt-90) cc_final: 0.7308 (ptt-90) REVERT: o 193 ARG cc_start: 0.7856 (ttp80) cc_final: 0.6855 (ttp-170) REVERT: o 197 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7135 (mt-10) REVERT: o 223 GLU cc_start: 0.7734 (tp30) cc_final: 0.7377 (tp30) REVERT: o 274 ASP cc_start: 0.6353 (t0) cc_final: 0.5573 (t70) REVERT: o 294 GLU cc_start: 0.6376 (tm-30) cc_final: 0.6171 (mt-10) REVERT: o 316 THR cc_start: 0.6930 (m) cc_final: 0.6674 (p) REVERT: o 321 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7046 (mp0) REVERT: o 347 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7199 (mm-30) REVERT: o 524 MET cc_start: 0.8257 (mmp) cc_final: 0.7684 (mmm) REVERT: o 556 GLU cc_start: 0.6423 (pt0) cc_final: 0.5914 (tp30) REVERT: o 612 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6750 (p0) REVERT: o 700 GLN cc_start: 0.6511 (tt0) cc_final: 0.5957 (tp-100) REVERT: o 711 GLN cc_start: 0.6363 (tt0) cc_final: 0.6154 (mm-40) REVERT: o 726 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7654 (mp0) REVERT: o 803 LYS cc_start: 0.7838 (tttp) cc_final: 0.7443 (tptp) REVERT: o 818 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7697 (mp0) REVERT: o 857 THR cc_start: 0.6744 (p) cc_final: 0.6386 (m) REVERT: o 919 LYS cc_start: 0.6735 (mttt) cc_final: 0.6475 (mmtp) REVERT: o 1133 LYS cc_start: 0.7528 (mttp) cc_final: 0.7310 (ptpp) REVERT: o 1146 GLN cc_start: 0.7836 (pp30) cc_final: 0.6744 (tp-100) REVERT: o 1153 ARG cc_start: 0.6986 (mmm-85) cc_final: 0.6562 (mmm-85) REVERT: o 1167 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7163 (ttm-80) REVERT: o 1279 MET cc_start: 0.6784 (mtm) cc_final: 0.6408 (tpp) REVERT: o 1286 ARG cc_start: 0.6868 (mtp85) cc_final: 0.6458 (mtp85) REVERT: o 1306 LYS cc_start: 0.6051 (mttt) cc_final: 0.5727 (mtpt) REVERT: o 1376 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5671 (ttmm) REVERT: o 1412 MET cc_start: 0.7633 (ttp) cc_final: 0.7170 (tmm) REVERT: o 1422 GLN cc_start: 0.6363 (mt0) cc_final: 0.5746 (mm110) REVERT: o 1437 ASP cc_start: 0.7363 (m-30) cc_final: 0.6812 (m-30) REVERT: o 1452 LYS cc_start: 0.7197 (mttt) cc_final: 0.6628 (mmtm) REVERT: p 53 MET cc_start: 0.6660 (mmm) cc_final: 0.6115 (mmm) REVERT: p 87 LYS cc_start: 0.7065 (tttt) cc_final: 0.6476 (tptt) REVERT: p 91 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6774 (tp) REVERT: p 152 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7308 (mm) REVERT: p 215 TYR cc_start: 0.7037 (m-80) cc_final: 0.6573 (m-80) REVERT: p 239 MET cc_start: 0.7028 (ttm) cc_final: 0.6755 (ttp) REVERT: p 298 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6331 (mtp) REVERT: p 313 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6989 (tm-30) REVERT: p 346 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6033 (mm-30) REVERT: p 381 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7730 (mp0) REVERT: p 388 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: p 420 GLN cc_start: 0.6047 (tt0) cc_final: 0.5653 (tp40) REVERT: p 438 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.5456 (ttp-110) REVERT: p 528 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (mt) REVERT: p 555 GLU cc_start: 0.7158 (pm20) cc_final: 0.6644 (tp30) REVERT: p 578 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7456 (mptt) REVERT: p 597 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7844 (mp) REVERT: p 629 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7043 (mt-10) REVERT: p 691 SER cc_start: 0.8256 (p) cc_final: 0.7782 (t) REVERT: p 728 MET cc_start: 0.7266 (mtm) cc_final: 0.6822 (mtp) REVERT: p 761 THR cc_start: 0.7774 (m) cc_final: 0.7475 (p) REVERT: p 796 MET cc_start: 0.8862 (mtm) cc_final: 0.8619 (mtm) REVERT: p 817 GLN cc_start: 0.8078 (pt0) cc_final: 0.7779 (pt0) REVERT: p 846 ASP cc_start: 0.8381 (m-30) cc_final: 0.8060 (p0) REVERT: p 850 ASP cc_start: 0.8113 (t0) cc_final: 0.7848 (p0) REVERT: p 1054 MET cc_start: 0.8364 (mtt) cc_final: 0.7938 (mtt) REVERT: p 1151 MET cc_start: 0.7755 (ptm) cc_final: 0.7319 (ptm) REVERT: q 17 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7359 (pt0) REVERT: q 24 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6704 (mt-10) REVERT: q 106 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6732 (ttm170) REVERT: q 109 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6264 (pm20) REVERT: q 110 ASP cc_start: 0.7998 (t0) cc_final: 0.7611 (m-30) REVERT: q 111 GLN cc_start: 0.8380 (tt0) cc_final: 0.7934 (mp10) REVERT: q 126 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6924 (mmm-85) REVERT: q 158 GLU cc_start: 0.7171 (tt0) cc_final: 0.6770 (pt0) REVERT: q 253 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6410 (ttmt) REVERT: q 265 HIS cc_start: 0.7237 (t70) cc_final: 0.6320 (t-170) REVERT: q 268 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6840 (tm-30) REVERT: s 49 SER cc_start: 0.8442 (t) cc_final: 0.8163 (p) REVERT: s 120 ASP cc_start: 0.6790 (m-30) cc_final: 0.6521 (m-30) REVERT: s 133 GLN cc_start: 0.7747 (mt0) cc_final: 0.7231 (tp-100) REVERT: t 81 VAL cc_start: 0.6396 (t) cc_final: 0.6137 (m) REVERT: t 86 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6266 (mm-30) REVERT: t 110 LEU cc_start: 0.7194 (mt) cc_final: 0.6900 (mt) REVERT: t 122 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6902 (mt-10) REVERT: u 104 MET cc_start: 0.5856 (tpp) cc_final: 0.5021 (tpt) REVERT: u 165 ASP cc_start: 0.6902 (t0) cc_final: 0.6679 (t0) REVERT: v 4 ILE cc_start: 0.8258 (mt) cc_final: 0.8033 (mm) REVERT: v 46 GLN cc_start: 0.7920 (mt0) cc_final: 0.7432 (tt0) REVERT: v 95 LYS cc_start: 0.7074 (tttt) cc_final: 0.6688 (ttpt) REVERT: v 100 GLU cc_start: 0.7973 (tt0) cc_final: 0.6913 (mt-10) REVERT: v 133 HIS cc_start: 0.7270 (p-80) cc_final: 0.6779 (m170) REVERT: w 18 GLN cc_start: 0.8444 (mt0) cc_final: 0.7989 (tm-30) REVERT: w 27 LYS cc_start: 0.7348 (ttpp) cc_final: 0.6891 (tttm) REVERT: w 68 ILE cc_start: 0.7675 (mt) cc_final: 0.7436 (mm) REVERT: w 71 ASP cc_start: 0.6957 (m-30) cc_final: 0.6684 (m-30) REVERT: w 93 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6444 (mm-30) REVERT: w 115 THR cc_start: 0.5996 (m) cc_final: 0.5380 (p) REVERT: y 23 LYS cc_start: 0.8204 (mttt) cc_final: 0.7662 (mptm) REVERT: y 55 GLN cc_start: 0.7612 (mt0) cc_final: 0.7266 (mt0) REVERT: y 70 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7065 (ttmt) REVERT: y 93 ASP cc_start: 0.7173 (m-30) cc_final: 0.6831 (m-30) REVERT: z 25 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7125 (mp0) REVERT: z 29 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7201 (mmpt) REVERT: z 35 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7320 (mtp85) REVERT: z 42 ARG cc_start: 0.7583 (mmt180) cc_final: 0.7339 (mtt180) REVERT: z 56 ASP cc_start: 0.7517 (m-30) cc_final: 0.7120 (p0) outliers start: 98 outliers final: 65 residues processed: 591 average time/residue: 1.6467 time to fit residues: 1152.2235 Evaluate side-chains 604 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 527 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1063 GLU Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 282 ARG Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 497 LYS Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1133 HIS Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 253 LYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain x residue 5 VAL Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.0020 chunk 399 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 419 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 333 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 265 GLN p 344 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN v 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36619 Z= 0.252 Angle : 0.470 10.007 49945 Z= 0.249 Chirality : 0.040 0.170 5562 Planarity : 0.003 0.054 6098 Dihedral : 15.993 155.005 5823 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.33 % Rotamer: Outliers : 2.55 % Allowed : 21.15 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.67 (0.13), residues: 4137 helix: 1.85 (0.14), residues: 1398 sheet: -0.18 (0.19), residues: 670 loop : -0.27 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o1334 HIS 0.006 0.001 HIS o 84 PHE 0.014 0.001 PHE p 320 TYR 0.017 0.001 TYR t 115 ARG 0.009 0.000 ARG o 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 527 time to evaluate : 4.127 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: o 16 ARG cc_start: 0.6992 (mmt90) cc_final: 0.6419 (mtt-85) REVERT: o 18 ILE cc_start: 0.8597 (mt) cc_final: 0.8270 (mm) REVERT: o 30 GLU cc_start: 0.6585 (tt0) cc_final: 0.6204 (tt0) REVERT: o 38 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7633 (mm-30) REVERT: o 58 MET cc_start: 0.7809 (ttp) cc_final: 0.7448 (ttp) REVERT: o 115 SER cc_start: 0.7184 (p) cc_final: 0.6853 (t) REVERT: o 192 ARG cc_start: 0.7643 (ptt-90) cc_final: 0.7363 (ptt-90) REVERT: o 193 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7357 (ttp-170) REVERT: o 197 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7167 (mt-10) REVERT: o 223 GLU cc_start: 0.7738 (tp30) cc_final: 0.7313 (tp30) REVERT: o 274 ASP cc_start: 0.6369 (t0) cc_final: 0.5583 (t70) REVERT: o 294 GLU cc_start: 0.6378 (tm-30) cc_final: 0.6175 (mt-10) REVERT: o 316 THR cc_start: 0.6760 (m) cc_final: 0.6469 (p) REVERT: o 321 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7015 (mp0) REVERT: o 347 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7233 (mm-30) REVERT: o 524 MET cc_start: 0.8256 (mmp) cc_final: 0.7694 (mmm) REVERT: o 556 GLU cc_start: 0.6388 (pt0) cc_final: 0.5906 (tp30) REVERT: o 612 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6750 (p0) REVERT: o 700 GLN cc_start: 0.6515 (tt0) cc_final: 0.5961 (tp-100) REVERT: o 711 GLN cc_start: 0.6359 (tt0) cc_final: 0.6152 (mm-40) REVERT: o 723 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7074 (m110) REVERT: o 726 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7685 (mp0) REVERT: o 803 LYS cc_start: 0.7831 (tttp) cc_final: 0.7436 (tptp) REVERT: o 818 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7689 (mp0) REVERT: o 919 LYS cc_start: 0.6645 (mttt) cc_final: 0.6420 (mmtp) REVERT: o 1104 LEU cc_start: 0.5079 (OUTLIER) cc_final: 0.4794 (mm) REVERT: o 1133 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7314 (ptpp) REVERT: o 1146 GLN cc_start: 0.7838 (pp30) cc_final: 0.6752 (tp-100) REVERT: o 1153 ARG cc_start: 0.6961 (mmm-85) cc_final: 0.6549 (mmm-85) REVERT: o 1167 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7146 (ttm-80) REVERT: o 1279 MET cc_start: 0.6783 (mtm) cc_final: 0.6404 (tpp) REVERT: o 1286 ARG cc_start: 0.6875 (mtp85) cc_final: 0.6467 (mtp85) REVERT: o 1306 LYS cc_start: 0.6044 (mttt) cc_final: 0.5698 (mtpt) REVERT: o 1376 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5678 (ttmm) REVERT: o 1412 MET cc_start: 0.7647 (ttp) cc_final: 0.7190 (tmm) REVERT: o 1422 GLN cc_start: 0.6367 (mt0) cc_final: 0.5743 (mm110) REVERT: o 1437 ASP cc_start: 0.7382 (m-30) cc_final: 0.6822 (m-30) REVERT: o 1452 LYS cc_start: 0.7069 (mttt) cc_final: 0.6449 (mmtm) REVERT: p 53 MET cc_start: 0.6665 (mmm) cc_final: 0.6122 (mmm) REVERT: p 87 LYS cc_start: 0.7072 (tttt) cc_final: 0.6504 (tptt) REVERT: p 91 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6851 (tp) REVERT: p 152 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7316 (mm) REVERT: p 215 TYR cc_start: 0.7033 (m-80) cc_final: 0.6555 (m-80) REVERT: p 239 MET cc_start: 0.7053 (ttm) cc_final: 0.6785 (ttp) REVERT: p 265 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: p 298 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6429 (mtp) REVERT: p 313 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6955 (tm-30) REVERT: p 381 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7732 (mp0) REVERT: p 388 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: p 420 GLN cc_start: 0.5986 (tt0) cc_final: 0.5557 (tp40) REVERT: p 438 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.5401 (ttp-110) REVERT: p 528 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7853 (mt) REVERT: p 578 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7242 (mptt) REVERT: p 597 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7874 (mp) REVERT: p 629 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7027 (mt-10) REVERT: p 691 SER cc_start: 0.8240 (p) cc_final: 0.7765 (t) REVERT: p 728 MET cc_start: 0.7192 (mtm) cc_final: 0.6748 (mtp) REVERT: p 761 THR cc_start: 0.7785 (m) cc_final: 0.7480 (p) REVERT: p 796 MET cc_start: 0.8866 (mtm) cc_final: 0.8620 (mtm) REVERT: p 817 GLN cc_start: 0.8056 (pt0) cc_final: 0.7759 (pt0) REVERT: p 846 ASP cc_start: 0.8380 (m-30) cc_final: 0.8062 (p0) REVERT: p 850 ASP cc_start: 0.8107 (t0) cc_final: 0.7835 (p0) REVERT: p 1151 MET cc_start: 0.7755 (ptm) cc_final: 0.7302 (ptm) REVERT: q 17 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7364 (pt0) REVERT: q 24 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6712 (mt-10) REVERT: q 106 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6744 (ttm170) REVERT: q 109 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6264 (pm20) REVERT: q 110 ASP cc_start: 0.7989 (t0) cc_final: 0.7634 (m-30) REVERT: q 111 GLN cc_start: 0.8385 (tt0) cc_final: 0.7938 (mp10) REVERT: q 126 ARG cc_start: 0.7444 (mtt180) cc_final: 0.6944 (mmm-85) REVERT: q 158 GLU cc_start: 0.7184 (tt0) cc_final: 0.6793 (pt0) REVERT: q 253 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6403 (ttmt) REVERT: q 265 HIS cc_start: 0.7351 (t70) cc_final: 0.6379 (t-170) REVERT: q 268 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6844 (tm-30) REVERT: s 49 SER cc_start: 0.8459 (t) cc_final: 0.8180 (p) REVERT: s 96 GLU cc_start: 0.8822 (tp30) cc_final: 0.8584 (tm-30) REVERT: s 120 ASP cc_start: 0.6797 (m-30) cc_final: 0.6528 (m-30) REVERT: s 133 GLN cc_start: 0.7749 (mt0) cc_final: 0.7226 (tp-100) REVERT: t 81 VAL cc_start: 0.6419 (t) cc_final: 0.6144 (m) REVERT: t 86 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6292 (mm-30) REVERT: t 110 LEU cc_start: 0.7191 (mt) cc_final: 0.6893 (mt) REVERT: t 122 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6917 (mt-10) REVERT: u 104 MET cc_start: 0.5846 (tpp) cc_final: 0.4983 (tpt) REVERT: v 4 ILE cc_start: 0.8256 (mt) cc_final: 0.8032 (mm) REVERT: v 46 GLN cc_start: 0.7921 (mt0) cc_final: 0.7425 (tt0) REVERT: v 95 LYS cc_start: 0.7226 (tttt) cc_final: 0.6737 (ttpt) REVERT: v 100 GLU cc_start: 0.7869 (tt0) cc_final: 0.6887 (mt-10) REVERT: v 133 HIS cc_start: 0.7271 (p-80) cc_final: 0.6780 (m170) REVERT: w 18 GLN cc_start: 0.8442 (mt0) cc_final: 0.8015 (tm-30) REVERT: w 27 LYS cc_start: 0.7435 (ttpp) cc_final: 0.7125 (tttm) REVERT: w 68 ILE cc_start: 0.7659 (mt) cc_final: 0.7435 (mm) REVERT: w 71 ASP cc_start: 0.6957 (m-30) cc_final: 0.6691 (m-30) REVERT: w 93 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6457 (mm-30) REVERT: w 115 THR cc_start: 0.5975 (m) cc_final: 0.5372 (p) REVERT: y 23 LYS cc_start: 0.8181 (mttt) cc_final: 0.7582 (mptm) REVERT: y 55 GLN cc_start: 0.7612 (mt0) cc_final: 0.7268 (mt0) REVERT: y 70 LYS cc_start: 0.7583 (ttpt) cc_final: 0.7074 (ttmt) REVERT: y 93 ASP cc_start: 0.7173 (m-30) cc_final: 0.6835 (m-30) REVERT: z 25 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7127 (mp0) REVERT: z 29 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7220 (mmpt) REVERT: z 35 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7607 (mtp85) REVERT: z 56 ASP cc_start: 0.7521 (m-30) cc_final: 0.7125 (p0) outliers start: 94 outliers final: 70 residues processed: 588 average time/residue: 1.6440 time to fit residues: 1150.2565 Evaluate side-chains 607 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 521 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 425 ASP Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 723 ASN Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1050 CYS Chi-restraints excluded: chain o residue 1063 GLU Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1167 ARG Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1376 LYS Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 61 ASP Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 152 ILE Chi-restraints excluded: chain p residue 198 GLU Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 265 GLN Chi-restraints excluded: chain p residue 282 ARG Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 395 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 438 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 497 LYS Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1076 GLU Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 253 LYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain x residue 5 VAL Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 0.0570 chunk 355 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 307 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 343 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 301 HIS ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 144 HIS p 265 GLN p 344 GLN ** p 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107107 restraints weight = 42117.774| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.52 r_work: 0.3159 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36619 Z= 0.175 Angle : 0.441 9.892 49945 Z= 0.235 Chirality : 0.039 0.167 5562 Planarity : 0.003 0.051 6098 Dihedral : 15.934 156.081 5823 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 2.49 % Allowed : 21.31 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.82 (0.13), residues: 4137 helix: 2.04 (0.14), residues: 1389 sheet: -0.11 (0.19), residues: 674 loop : -0.22 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP o1334 HIS 0.005 0.001 HIS o 84 PHE 0.019 0.001 PHE o 234 TYR 0.017 0.001 TYR u 167 ARG 0.009 0.000 ARG o 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18522.53 seconds wall clock time: 326 minutes 10.08 seconds (19570.08 seconds total)