Starting phenix.real_space_refine on Wed Mar 20 21:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/03_2024/8ree_19084.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 17615 2.51 5 N 5066 2.21 5 O 5722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 588": "OE1" <-> "OE2" Residue "C GLU 602": "OE1" <-> "OE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C GLU 775": "OE1" <-> "OE2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "C ASP 1088": "OD1" <-> "OD2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1188": "OD1" <-> "OD2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 699": "OD1" <-> "OD2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D ASP 813": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 1146": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28605 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2103 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 280 Chain: "N" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 917 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "R" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14675 SG CYS D 70 107.768 114.567 86.352 1.00 46.88 S ATOM 14804 SG CYS D 88 106.510 115.411 90.421 1.00 47.95 S ATOM 20917 SG CYS D 898 100.880 47.137 83.808 1.00 25.68 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.89 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.89 Time building chain proxies: 14.55, per 1000 atoms: 0.51 Number of scatterers: 28605 At special positions: 0 Unit cell: (141.504, 171.52, 167.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 96 16.00 P 103 15.00 Mg 1 11.99 O 5722 8.00 N 5066 7.00 C 17615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.20 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 44 sheets defined 39.3% alpha, 13.7% beta 42 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 9.08 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.780A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.588A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.586A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.769A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.799A pdb=" N LEU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.532A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.789A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.778A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.852A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.724A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.745A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.640A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.671A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.698A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.648A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 4.049A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 481 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.595A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.718A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.789A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.947A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.637A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.739A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.835A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 removed outlier: 3.563A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.604A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.196A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.514A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.982A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.631A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.805A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.541A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.925A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.638A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.274A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.603A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.863A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.586A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.213A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.732A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.621A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.784A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.608A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.906A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.573A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 4.076A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.768A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 4.150A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.085A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.634A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.663A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 123 through 131 removed outlier: 3.918A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 172 through 184 Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.302A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 223 removed outlier: 3.676A pdb=" N ILE M 220 " --> pdb=" O ALA M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 3.916A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 256 removed outlier: 4.089A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 256 " --> pdb=" O LEU M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 294 removed outlier: 3.895A pdb=" N SER M 293 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU M 294 " --> pdb=" O SER M 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 290 through 294' Processing helix chain 'M' and resid 341 through 355 removed outlier: 3.501A pdb=" N PHE M 354 " --> pdb=" O GLN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.576A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 457 through 466 removed outlier: 3.820A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER M 466 " --> pdb=" O ARG M 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.562A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 7.320A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.626A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.530A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 5.584A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.937A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.549A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.968A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.603A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.603A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.065A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.699A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.699A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.651A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 723 through 727 removed outlier: 7.016A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.677A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.627A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.627A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.426A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.993A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.684A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 523 through 527 removed outlier: 4.407A pdb=" N GLU D 523 " --> pdb=" O ARG D 547 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LYS D 549 " --> pdb=" O GLU D 523 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET D 525 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG D 551 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.044A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.805A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.517A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.690A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 5.006A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1265 through 1266 1100 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 14.04 Time building geometry restraints manager: 12.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8966 1.34 - 1.46: 4229 1.46 - 1.58: 15657 1.58 - 1.70: 205 1.70 - 1.81: 167 Bond restraints: 29224 Sorted by residual: bond pdb=" CB PRO D1185 " pdb=" CG PRO D1185 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.43e+00 bond pdb=" CB PRO C1317 " pdb=" CG PRO C1317 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.59e+00 bond pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.49e+00 bond pdb=" CB PRO C 205 " pdb=" CG PRO C 205 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.35e+00 bond pdb=" CG PRO C1317 " pdb=" CD PRO C1317 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 2.99e+00 ... (remaining 29219 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.51: 939 105.51 - 112.66: 15934 112.66 - 119.81: 9595 119.81 - 126.96: 13217 126.96 - 134.11: 469 Bond angle restraints: 40154 Sorted by residual: angle pdb=" CA PRO D1185 " pdb=" N PRO D1185 " pdb=" CD PRO D1185 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.71e+01 angle pdb=" C LEU M 277 " pdb=" N VAL M 278 " pdb=" CA VAL M 278 " ideal model delta sigma weight residual 121.97 131.72 -9.75 1.80e+00 3.09e-01 2.93e+01 angle pdb=" CA PRO C1317 " pdb=" N PRO C1317 " pdb=" CD PRO C1317 " ideal model delta sigma weight residual 112.00 105.49 6.51 1.40e+00 5.10e-01 2.16e+01 angle pdb=" CA PRO C 205 " pdb=" N PRO C 205 " pdb=" CD PRO C 205 " ideal model delta sigma weight residual 112.00 106.10 5.90 1.40e+00 5.10e-01 1.77e+01 angle pdb=" N ASP D 751 " pdb=" CA ASP D 751 " pdb=" C ASP D 751 " ideal model delta sigma weight residual 114.75 109.49 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 40149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 16515 34.83 - 69.65: 977 69.65 - 104.48: 55 104.48 - 139.31: 1 139.31 - 174.14: 3 Dihedral angle restraints: 17551 sinusoidal: 7160 harmonic: 10391 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 142.99 37.01 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" CA VAL M 278 " pdb=" C VAL M 278 " pdb=" N ARG M 279 " pdb=" CA ARG M 279 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ILE D 331 " pdb=" C ILE D 331 " pdb=" N LYS D 332 " pdb=" CA LYS D 332 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 17548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3334 0.036 - 0.072: 1001 0.072 - 0.109: 371 0.109 - 0.145: 77 0.145 - 0.181: 5 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB VAL M 278 " pdb=" CA VAL M 278 " pdb=" CG1 VAL M 278 " pdb=" CG2 VAL M 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CB ILE M 170 " pdb=" CA ILE M 170 " pdb=" CG1 ILE M 170 " pdb=" CG2 ILE M 170 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CG LEU B 133 " pdb=" CB LEU B 133 " pdb=" CD1 LEU B 133 " pdb=" CD2 LEU B 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 4785 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 567 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D1184 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO D1185 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO D1185 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D1185 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO C 205 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.059 5.00e-02 4.00e+02 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 172 2.53 - 3.12: 21462 3.12 - 3.71: 44955 3.71 - 4.31: 57724 4.31 - 4.90: 97826 Nonbonded interactions: 222139 Sorted by model distance: nonbonded pdb=" O3' C R 7 " pdb="MG MG D1501 " model vdw 1.936 2.170 nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.127 2.230 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.147 2.170 nonbonded pdb=" OD1 ASP C 354 " pdb=" OG1 THR C 356 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.157 2.170 ... (remaining 222134 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.030 Extract box with map and model: 3.300 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 84.940 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3640 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 : 0.003 0.105 29224 Z= 0.226 Angle : 0.644 14.474 40154 Z= 0.337 Chirality : 0.041 0.181 4788 Planarity : 0.005 0.124 4906 Dihedral : 19.576 174.137 10845 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 0.38 % Allowed : 31.31 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 (0.14), residues: 3587 helix: 0.91 (0.15), residues: 1242 sheet: -0.26 (0.28), residues: 373 loop : -1.49 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 183 HIS 0.010 0.001 HIS D 651 PHE 0.020 0.001 PHE D 668 TYR 0.014 0.001 TYR C 73 ARG 0.013 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 773 time to evaluate : 3.026 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: 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: B 92 VAL cc_start: 0.5819 (m) cc_final: 0.5579 (t) REVERT: C 239 MET cc_start: 0.3754 (tpt) cc_final: 0.3442 (tpp) REVERT: C 622 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.5213 (m110) REVERT: C 693 LEU cc_start: 0.4849 (mt) cc_final: 0.4638 (mt) REVERT: C 1225 VAL cc_start: 0.5763 (t) cc_final: 0.5547 (t) outliers start: 10 outliers final: 0 residues processed: 777 average time/residue: 0.4498 time to fit residues: 524.2452 Evaluate side-chains 454 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 622 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 154 optimal weight: 50.0000 chunk 95 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 333 optimal weight: 50.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 658 GLN C 659 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1312 ASN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN M 262 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 29224 Z= 0.530 Angle : 1.156 20.462 40154 Z= 0.598 Chirality : 0.057 0.271 4788 Planarity : 0.010 0.131 4906 Dihedral : 16.877 176.932 5050 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 10.54 % Allowed : 27.00 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: -2.16 (0.13), residues: 3587 helix: -0.91 (0.13), residues: 1272 sheet: -0.62 (0.26), residues: 370 loop : -2.00 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 33 HIS 0.020 0.004 HIS A 66 PHE 0.048 0.005 PHE C 828 TYR 0.048 0.004 TYR C 62 ARG 0.023 0.002 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 556 time to evaluate : 2.928 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.4873 (mm) cc_final: 0.4575 (mm) REVERT: B 14 VAL cc_start: 0.7132 (m) cc_final: 0.6800 (m) REVERT: B 177 TYR cc_start: 0.5584 (m-80) cc_final: 0.5320 (m-80) REVERT: C 79 VAL cc_start: 0.5788 (OUTLIER) cc_final: 0.5351 (t) REVERT: C 195 PHE cc_start: 0.2781 (OUTLIER) cc_final: 0.2054 (m-10) REVERT: C 292 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5990 (tt) REVERT: C 1229 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7023 (t80) REVERT: C 1273 MET cc_start: 0.3281 (ptm) cc_final: 0.2588 (mpp) REVERT: D 648 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7034 (mm-30) REVERT: D 1220 ILE cc_start: 0.7895 (mt) cc_final: 0.7679 (mt) REVERT: E 48 VAL cc_start: 0.6295 (OUTLIER) cc_final: 0.5989 (p) REVERT: M 262 GLN cc_start: 0.2058 (OUTLIER) cc_final: 0.1753 (tt0) outliers start: 276 outliers final: 97 residues processed: 770 average time/residue: 0.3954 time to fit residues: 490.6267 Evaluate side-chains 515 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 412 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 292 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 333 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 331 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 267 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 268 ASN C 31 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1312 ASN C1324 ASN D 80 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 450 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 489 ASN D 921 GLN E 31 GLN M 262 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 29224 Z= 0.312 Angle : 0.758 12.500 40154 Z= 0.391 Chirality : 0.046 0.238 4788 Planarity : 0.006 0.083 4906 Dihedral : 16.629 175.375 5048 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 6.64 % Allowed : 30.55 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3587 helix: 0.13 (0.14), residues: 1296 sheet: -0.26 (0.27), residues: 372 loop : -1.85 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 183 HIS 0.007 0.001 HIS D 113 PHE 0.043 0.002 PHE C 934 TYR 0.023 0.002 TYR C1305 ARG 0.023 0.001 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 445 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 488 MET cc_start: 0.3511 (mtt) cc_final: 0.2963 (mtt) REVERT: C 753 LEU cc_start: 0.7181 (mp) cc_final: 0.6950 (mp) REVERT: C 773 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6332 (tt) REVERT: C 892 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.2956 (pm20) REVERT: C 1180 MET cc_start: 0.7907 (tpp) cc_final: 0.6871 (tpt) REVERT: C 1289 GLU cc_start: 0.5303 (tm-30) cc_final: 0.5070 (tm-30) REVERT: C 1319 MET cc_start: 0.6309 (tpp) cc_final: 0.5709 (tpp) REVERT: D 377 PHE cc_start: 0.7385 (m-80) cc_final: 0.7099 (m-10) REVERT: D 993 GLU cc_start: 0.1755 (mt-10) cc_final: 0.1039 (mt-10) REVERT: D 1145 PHE cc_start: 0.7572 (m-80) cc_final: 0.7226 (m-10) REVERT: E 42 GLU cc_start: 0.6976 (mp0) cc_final: 0.6463 (mp0) outliers start: 174 outliers final: 84 residues processed: 576 average time/residue: 0.3474 time to fit residues: 334.3411 Evaluate side-chains 455 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 369 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 20.0000 chunk 251 optimal weight: 0.4980 chunk 173 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 75 GLN A 186 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 277 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.9295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29224 Z= 0.193 Angle : 0.672 10.314 40154 Z= 0.339 Chirality : 0.043 0.216 4788 Planarity : 0.005 0.077 4906 Dihedral : 16.487 175.558 5048 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 4.81 % Allowed : 32.34 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3587 helix: 0.36 (0.14), residues: 1313 sheet: -0.09 (0.27), residues: 382 loop : -1.79 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.003 0.001 HIS M 391 PHE 0.017 0.001 PHE C 390 TYR 0.019 0.001 TYR C 62 ARG 0.006 0.001 ARG C 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 383 time to evaluate : 3.163 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: A 48 LEU cc_start: 0.8218 (tp) cc_final: 0.8016 (tp) REVERT: C 456 VAL cc_start: 0.8296 (p) cc_final: 0.8077 (p) REVERT: C 1319 MET cc_start: 0.6810 (tpp) cc_final: 0.6028 (tpp) REVERT: D 29 MET cc_start: 0.5382 (ttm) cc_final: 0.5125 (ttp) outliers start: 126 outliers final: 75 residues processed: 475 average time/residue: 0.3231 time to fit residues: 262.8285 Evaluate side-chains 427 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 352 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 302 optimal weight: 0.2980 chunk 245 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 89 optimal weight: 40.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 517 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN C1324 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 1.0396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29224 Z= 0.254 Angle : 0.679 10.185 40154 Z= 0.347 Chirality : 0.043 0.211 4788 Planarity : 0.005 0.070 4906 Dihedral : 16.427 176.404 5048 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 6.15 % Allowed : 30.89 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3587 helix: 0.47 (0.14), residues: 1301 sheet: -0.13 (0.27), residues: 373 loop : -1.74 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 183 HIS 0.003 0.001 HIS C 551 PHE 0.020 0.002 PHE M 402 TYR 0.019 0.001 TYR C 179 ARG 0.006 0.001 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 359 time to evaluate : 3.057 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: A 205 MET cc_start: 0.6889 (tmm) cc_final: 0.6558 (ttp) REVERT: A 262 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.3996 (mm) REVERT: B 97 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: C 653 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.4609 (tpt) REVERT: C 1098 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8558 (mm) REVERT: C 1329 GLU cc_start: 0.5249 (tt0) cc_final: 0.4937 (tt0) REVERT: D 993 GLU cc_start: 0.1295 (mt-10) cc_final: 0.1016 (mt-10) REVERT: M 220 ILE cc_start: 0.7898 (mm) cc_final: 0.7527 (mm) REVERT: M 271 TYR cc_start: 0.4001 (OUTLIER) cc_final: 0.3304 (m-80) outliers start: 161 outliers final: 100 residues processed: 476 average time/residue: 0.3351 time to fit residues: 271.9564 Evaluate side-chains 441 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 336 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 355 optimal weight: 40.0000 chunk 294 optimal weight: 40.0000 chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 799 ASN C 824 GLN C 856 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN ** D1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 1.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 29224 Z= 0.358 Angle : 0.789 21.454 40154 Z= 0.407 Chirality : 0.046 0.318 4788 Planarity : 0.006 0.081 4906 Dihedral : 16.632 177.558 5048 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 6.95 % Allowed : 30.81 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3587 helix: 0.21 (0.14), residues: 1301 sheet: -0.29 (0.27), residues: 376 loop : -1.74 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1276 HIS 0.005 0.001 HIS B 23 PHE 0.029 0.002 PHE C 464 TYR 0.034 0.002 TYR A 68 ARG 0.037 0.001 ARG C1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 315 time to evaluate : 3.277 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: C 892 GLU cc_start: 0.4561 (OUTLIER) cc_final: 0.2823 (pm20) REVERT: C 1107 MET cc_start: 0.8148 (mpp) cc_final: 0.7413 (mtm) REVERT: C 1230 MET cc_start: 0.7617 (tmm) cc_final: 0.6951 (ttt) REVERT: D 330 MET cc_start: 0.6750 (ppp) cc_final: 0.5886 (ppp) REVERT: D 429 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8458 (mt) REVERT: D 472 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7800 (pp) REVERT: D 641 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 698 MET cc_start: 0.7945 (mmm) cc_final: 0.7670 (tpp) REVERT: E 30 MET cc_start: 0.7613 (mmt) cc_final: 0.7271 (tpt) REVERT: M 271 TYR cc_start: 0.4117 (OUTLIER) cc_final: 0.3060 (m-80) outliers start: 182 outliers final: 111 residues processed: 466 average time/residue: 0.3487 time to fit residues: 274.4478 Evaluate side-chains 386 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 270 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 202 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 198 optimal weight: 1.9990 chunk 353 optimal weight: 50.0000 chunk 221 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 1.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29224 Z= 0.257 Angle : 0.694 15.494 40154 Z= 0.354 Chirality : 0.043 0.185 4788 Planarity : 0.004 0.067 4906 Dihedral : 16.521 176.325 5048 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 5.50 % Allowed : 33.14 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3587 helix: 0.47 (0.14), residues: 1296 sheet: -0.10 (0.27), residues: 366 loop : -1.62 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 285 HIS 0.005 0.001 HIS M 391 PHE 0.015 0.001 PHE E 17 TYR 0.018 0.001 TYR D 269 ARG 0.007 0.001 ARG D1369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 279 time to evaluate : 2.874 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: C 453 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8356 (tp) REVERT: C 758 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7992 (ttt90) REVERT: C 864 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5685 (mtmm) REVERT: C 1107 MET cc_start: 0.8111 (mpp) cc_final: 0.7435 (mtm) REVERT: C 1230 MET cc_start: 0.7865 (tmm) cc_final: 0.6991 (ttt) REVERT: D 429 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8449 (mt) REVERT: D 641 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (tp) REVERT: D 698 MET cc_start: 0.7946 (mmm) cc_final: 0.7737 (tpp) REVERT: D 821 MET cc_start: 0.6439 (mmp) cc_final: 0.5799 (mmp) REVERT: M 271 TYR cc_start: 0.4023 (OUTLIER) cc_final: 0.2949 (m-80) outliers start: 144 outliers final: 99 residues processed: 401 average time/residue: 0.3562 time to fit residues: 238.6745 Evaluate side-chains 360 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 255 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 1.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 29224 Z= 0.295 Angle : 0.703 15.782 40154 Z= 0.361 Chirality : 0.044 0.388 4788 Planarity : 0.005 0.070 4906 Dihedral : 16.515 176.960 5048 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 5.38 % Allowed : 33.22 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3587 helix: 0.45 (0.14), residues: 1297 sheet: -0.32 (0.27), residues: 379 loop : -1.63 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 868 HIS 0.004 0.001 HIS B 23 PHE 0.015 0.002 PHE C1270 TYR 0.021 0.002 TYR D 995 ARG 0.007 0.001 ARG M 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 260 time to evaluate : 3.141 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: C 453 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8473 (tp) REVERT: C 758 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7773 (ttt90) REVERT: C 864 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6136 (mtmm) REVERT: C 1107 MET cc_start: 0.8137 (mpp) cc_final: 0.7441 (mtm) REVERT: C 1230 MET cc_start: 0.7608 (tmm) cc_final: 0.6866 (ttt) REVERT: C 1243 MET cc_start: 0.8924 (tmm) cc_final: 0.8404 (tmm) REVERT: D 429 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8424 (mt) REVERT: D 438 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: D 995 TYR cc_start: 0.5906 (m-80) cc_final: 0.5552 (m-80) REVERT: M 137 ASP cc_start: 0.5383 (OUTLIER) cc_final: 0.5140 (m-30) REVERT: M 271 TYR cc_start: 0.4069 (OUTLIER) cc_final: 0.3134 (m-80) outliers start: 141 outliers final: 105 residues processed: 379 average time/residue: 0.3686 time to fit residues: 233.8245 Evaluate side-chains 352 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 240 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 4.9990 chunk 338 optimal weight: 50.0000 chunk 309 optimal weight: 20.0000 chunk 329 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 311 optimal weight: 30.0000 chunk 328 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 41 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 1.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 29224 Z= 0.431 Angle : 0.828 14.728 40154 Z= 0.430 Chirality : 0.048 0.248 4788 Planarity : 0.006 0.086 4906 Dihedral : 16.753 178.435 5048 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.34 % Favored : 91.58 % Rotamer: Outliers : 5.50 % Allowed : 32.72 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3587 helix: 0.09 (0.14), residues: 1304 sheet: -0.45 (0.26), residues: 383 loop : -1.82 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 126 HIS 0.005 0.001 HIS D 113 PHE 0.047 0.003 PHE C1270 TYR 0.029 0.002 TYR C 395 ARG 0.017 0.001 ARG D 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 235 time to evaluate : 3.456 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: C 138 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (pt) REVERT: C 301 TYR cc_start: 0.1328 (OUTLIER) cc_final: -0.0397 (p90) REVERT: C 453 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8560 (tp) REVERT: C 530 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7646 (tp) REVERT: C 542 ARG cc_start: 0.5702 (mmt-90) cc_final: 0.5022 (mmt-90) REVERT: C 758 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8009 (ttt90) REVERT: C 864 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6891 (mtmm) REVERT: C 1107 MET cc_start: 0.8187 (mpp) cc_final: 0.7627 (mtm) REVERT: C 1230 MET cc_start: 0.7505 (tmm) cc_final: 0.6889 (ttt) REVERT: D 92 VAL cc_start: 0.4808 (OUTLIER) cc_final: 0.4515 (p) REVERT: D 115 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7044 (m-90) REVERT: D 237 MET cc_start: 0.7636 (mmm) cc_final: 0.7190 (tpp) REVERT: D 238 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8627 (pt) REVERT: D 330 MET cc_start: 0.7146 (ppp) cc_final: 0.6771 (ppp) REVERT: D 429 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8409 (mt) REVERT: D 485 MET cc_start: 0.7178 (mmm) cc_final: 0.6646 (mmp) REVERT: D 821 MET cc_start: 0.6686 (mmp) cc_final: 0.6413 (mmm) REVERT: D 822 MET cc_start: 0.7084 (mmm) cc_final: 0.6860 (mmm) REVERT: D 1190 ILE cc_start: 0.8692 (mm) cc_final: 0.8457 (pt) REVERT: M 137 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: M 271 TYR cc_start: 0.4571 (OUTLIER) cc_final: 0.3942 (m-80) outliers start: 144 outliers final: 92 residues processed: 355 average time/residue: 0.3520 time to fit residues: 210.6798 Evaluate side-chains 309 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 205 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 9.9990 chunk 348 optimal weight: 50.0000 chunk 212 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 365 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 291 optimal weight: 50.0000 chunk 30 optimal weight: 0.0070 chunk 224 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 1.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29224 Z= 0.284 Angle : 0.736 14.735 40154 Z= 0.377 Chirality : 0.044 0.195 4788 Planarity : 0.005 0.073 4906 Dihedral : 16.653 177.217 5048 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 3.82 % Allowed : 34.71 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3587 helix: 0.29 (0.14), residues: 1298 sheet: -0.22 (0.28), residues: 353 loop : -1.70 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 33 HIS 0.038 0.001 HIS A 23 PHE 0.023 0.002 PHE C1270 TYR 0.020 0.002 TYR D 995 ARG 0.019 0.001 ARG M 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 226 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 453 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 758 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7867 (ttt90) REVERT: C 1107 MET cc_start: 0.8176 (mpp) cc_final: 0.7630 (mtm) REVERT: C 1230 MET cc_start: 0.7450 (tmm) cc_final: 0.6886 (ttt) REVERT: D 115 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6790 (m-90) REVERT: D 130 MET cc_start: 0.8398 (mpp) cc_final: 0.8088 (pmm) REVERT: D 237 MET cc_start: 0.7499 (mmm) cc_final: 0.7172 (tpp) REVERT: D 485 MET cc_start: 0.7041 (mmm) cc_final: 0.6781 (mmp) REVERT: D 821 MET cc_start: 0.6575 (mmp) cc_final: 0.6302 (mmm) REVERT: E 18 ASP cc_start: 0.6566 (p0) cc_final: 0.6127 (p0) REVERT: M 137 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: M 248 GLU cc_start: 0.6653 (pm20) cc_final: 0.6131 (pm20) REVERT: M 271 TYR cc_start: 0.4710 (OUTLIER) cc_final: 0.3911 (m-80) outliers start: 100 outliers final: 77 residues processed: 308 average time/residue: 0.3596 time to fit residues: 184.0335 Evaluate side-chains 284 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 202 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 376 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 4.9990 chunk 310 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 268 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 299 optimal weight: 50.0000 chunk 36 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055107 restraints weight = 128438.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.056700 restraints weight = 66004.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057762 restraints weight = 43459.908| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 1.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29224 Z= 0.249 Angle : 0.734 15.412 40154 Z= 0.369 Chirality : 0.044 0.243 4788 Planarity : 0.005 0.067 4906 Dihedral : 16.596 176.870 5048 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 3.28 % Allowed : 35.05 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3587 helix: 0.40 (0.14), residues: 1301 sheet: -0.19 (0.28), residues: 352 loop : -1.67 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.017 0.001 HIS A 23 PHE 0.023 0.001 PHE C1270 TYR 0.028 0.002 TYR C1281 ARG 0.008 0.001 ARG M 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6109.54 seconds wall clock time: 110 minutes 39.59 seconds (6639.59 seconds total)