Starting phenix.real_space_refine on Sat Aug 10 04:31:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/08_2024/8ree_19084.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/08_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_19084/08_2024/8ree_19084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/08_2024/8ree_19084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/08_2024/8ree_19084.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ree_19084/08_2024/8ree_19084.cif" } 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: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 14.30, per 1000 atoms: 0.50 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: 10.92 Conformation dependent library (CDL) restraints added in 4.8 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: 9.33 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: 13.59 Time building geometry restraints manager: 11.95 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 3.040 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 Time spend for trying shortcut: 0.00 ========== 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: 0.400 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 83.910 Find NCS groups from input model: 0.630 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.030 ------------------------------------------------------------------------------- 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 : 3.106 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: 0.4556 time to fit residues: 530.1748 Evaluate side-chains 454 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 2.864 ------------------------------------------------------------------------------- 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: 0.3980 chunk 278 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 187 optimal weight: 0.1980 chunk 148 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 A 268 ASN B 227 GLN C 517 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 965 GLN C1237 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1197 ASN D1350 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4278 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29224 Z= 0.222 Angle : 0.719 11.436 40154 Z= 0.367 Chirality : 0.044 0.315 4788 Planarity : 0.005 0.088 4906 Dihedral : 16.346 174.701 5050 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 5.31 % Allowed : 29.59 % Favored : 65.10 % 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: -0.66 (0.14), residues: 3587 helix: 0.87 (0.15), residues: 1276 sheet: -0.02 (0.28), residues: 366 loop : -1.47 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.009 0.001 HIS D 469 PHE 0.022 0.002 PHE C 57 TYR 0.041 0.002 TYR C 62 ARG 0.007 0.001 ARG C 54 *********************** 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 637 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 498 time to evaluate : 3.074 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 77 ASP cc_start: 0.4685 (OUTLIER) cc_final: 0.4450 (t0) REVERT: C 1098 LEU cc_start: 0.2945 (OUTLIER) cc_final: 0.2491 (mp) REVERT: C 1229 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6211 (t80) REVERT: C 1235 LEU cc_start: 0.4995 (OUTLIER) cc_final: 0.4643 (mp) REVERT: D 993 GLU cc_start: 0.0773 (mt-10) cc_final: -0.0762 (mt-10) REVERT: E 59 ILE cc_start: 0.3230 (OUTLIER) cc_final: 0.1996 (mm) outliers start: 139 outliers final: 44 residues processed: 599 average time/residue: 0.3892 time to fit residues: 374.1763 Evaluate side-chains 463 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 414 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 277 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 333 optimal weight: 50.0000 chunk 360 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 186 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 658 GLN C 761 GLN C1080 ASN C1256 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 29224 Z= 0.349 Angle : 0.807 12.613 40154 Z= 0.416 Chirality : 0.047 0.248 4788 Planarity : 0.006 0.098 4906 Dihedral : 16.417 176.244 5048 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 6.26 % Allowed : 28.26 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.97 (0.14), residues: 3587 helix: 0.49 (0.14), residues: 1292 sheet: -0.12 (0.28), residues: 369 loop : -1.60 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 686 HIS 0.016 0.002 HIS D 113 PHE 0.030 0.003 PHE D 719 TYR 0.037 0.003 TYR C 123 ARG 0.029 0.001 ARG D1231 *********************** 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 658 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 494 time to evaluate : 3.045 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: A 307 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4828 (mt) REVERT: B 82 LEU cc_start: 0.9160 (mt) cc_final: 0.8894 (mm) REVERT: C 414 ILE cc_start: 0.5527 (tt) cc_final: 0.4280 (tt) REVERT: C 517 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.5414 (mm110) REVERT: C 921 PRO cc_start: 0.7213 (Cg_exo) cc_final: 0.6998 (Cg_endo) REVERT: C 1131 MET cc_start: 0.5706 (ptp) cc_final: 0.5341 (ptp) REVERT: C 1273 MET cc_start: 0.2768 (ptm) cc_final: 0.0957 (mpp) REVERT: D 314 ARG cc_start: 0.1651 (pmt-80) cc_final: 0.1185 (pmt-80) REVERT: D 899 TYR cc_start: 0.6192 (t80) cc_final: 0.5980 (t80) REVERT: D 993 GLU cc_start: 0.1661 (mt-10) cc_final: 0.1379 (mt-10) REVERT: D 1220 ILE cc_start: 0.7557 (mt) cc_final: 0.7356 (mt) REVERT: D 1340 LYS cc_start: 0.3731 (OUTLIER) cc_final: 0.3376 (pttp) REVERT: M 144 ILE cc_start: 0.3588 (OUTLIER) cc_final: 0.2860 (pt) REVERT: M 406 HIS cc_start: 0.4011 (OUTLIER) cc_final: 0.2810 (m90) outliers start: 164 outliers final: 76 residues processed: 609 average time/residue: 0.3954 time to fit residues: 397.6973 Evaluate side-chains 478 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 397 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 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 307 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU 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 82 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU 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 783 LEU Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 841 ARG 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 1182 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 357 GLN Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 30.0000 chunk 251 optimal weight: 0.8980 chunk 173 optimal weight: 0.1980 chunk 36 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 335 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 175 optimal weight: 0.3980 chunk 317 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 186 ASN C 568 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1080 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN E 31 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29224 Z= 0.194 Angle : 0.671 11.058 40154 Z= 0.341 Chirality : 0.043 0.189 4788 Planarity : 0.005 0.076 4906 Dihedral : 16.338 175.816 5048 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 5.04 % Allowed : 30.39 % Favored : 64.57 % 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: -0.74 (0.14), residues: 3587 helix: 0.80 (0.15), residues: 1281 sheet: -0.08 (0.27), residues: 379 loop : -1.53 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 236 HIS 0.004 0.001 HIS D 469 PHE 0.019 0.002 PHE C 15 TYR 0.022 0.002 TYR C 756 ARG 0.007 0.001 ARG D 278 *********************** 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 565 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 433 time to evaluate : 3.357 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: A 307 LEU cc_start: 0.5006 (OUTLIER) cc_final: 0.4727 (mt) REVERT: B 82 LEU cc_start: 0.9102 (mt) cc_final: 0.8853 (mm) REVERT: C 773 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4753 (mt) REVERT: C 1273 MET cc_start: 0.2416 (ptm) cc_final: 0.0945 (mpp) REVERT: E 48 VAL cc_start: 0.5495 (OUTLIER) cc_final: 0.5260 (p) outliers start: 132 outliers final: 71 residues processed: 527 average time/residue: 0.3559 time to fit residues: 318.3607 Evaluate side-chains 467 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 393 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR 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 144 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1070 HIS 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 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1303 SER 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 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 287 VAL 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: 5.9990 chunk 201 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 302 optimal weight: 40.0000 chunk 245 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 686 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 262 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.9007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29224 Z= 0.330 Angle : 0.813 20.329 40154 Z= 0.422 Chirality : 0.047 0.513 4788 Planarity : 0.006 0.146 4906 Dihedral : 16.444 176.585 5048 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.75 % Favored : 93.17 % Rotamer: Outliers : 6.49 % Allowed : 28.52 % Favored : 64.99 % Cbeta Deviations : 0.03 % 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: -1.08 (0.14), residues: 3587 helix: 0.48 (0.14), residues: 1294 sheet: -0.44 (0.27), residues: 361 loop : -1.66 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 33 HIS 0.084 0.003 HIS C1070 PHE 0.045 0.003 PHE C1270 TYR 0.029 0.002 TYR C 605 ARG 0.037 0.001 ARG C1269 *********************** 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 608 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 438 time to evaluate : 2.998 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 773 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6313 (mt) REVERT: C 1069 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7616 (ptt-90) REVERT: D 130 MET cc_start: 0.3880 (mpp) cc_final: 0.3552 (mpp) REVERT: D 445 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8441 (tppp) REVERT: D 993 GLU cc_start: 0.1382 (mt-10) cc_final: 0.0638 (mt-10) REVERT: D 1344 LEU cc_start: 0.7019 (mp) cc_final: 0.6815 (mp) REVERT: M 220 ILE cc_start: 0.7882 (mm) cc_final: 0.7506 (mm) REVERT: M 262 GLN cc_start: 0.1727 (OUTLIER) cc_final: 0.1468 (tt0) outliers start: 170 outliers final: 85 residues processed: 560 average time/residue: 0.3583 time to fit residues: 335.1099 Evaluate side-chains 460 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 371 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL 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 144 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU 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 C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 858 VAL 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 1249 ASN Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 0.0870 chunk 319 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 87 optimal weight: 0.0980 chunk 355 optimal weight: 50.0000 chunk 294 optimal weight: 50.0000 chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 186 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN C1220 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 GLN M 262 GLN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.9536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29224 Z= 0.211 Angle : 0.698 12.736 40154 Z= 0.353 Chirality : 0.043 0.218 4788 Planarity : 0.005 0.074 4906 Dihedral : 16.388 175.769 5048 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 3.93 % Allowed : 32.53 % Favored : 63.54 % 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: -0.88 (0.14), residues: 3587 helix: 0.69 (0.14), residues: 1306 sheet: -0.38 (0.27), residues: 360 loop : -1.58 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1276 HIS 0.017 0.001 HIS C1070 PHE 0.026 0.002 PHE E 17 TYR 0.040 0.002 TYR C1281 ARG 0.011 0.001 ARG D 297 *********************** 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 507 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 404 time to evaluate : 3.064 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: D 130 MET cc_start: 0.4135 (mpp) cc_final: 0.3739 (mpp) REVERT: E 16 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7003 (ttp80) outliers start: 103 outliers final: 71 residues processed: 470 average time/residue: 0.3424 time to fit residues: 271.8080 Evaluate side-chains 440 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 369 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 133 LEU 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 C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 498 ILE 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 605 TYR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1335 ILE 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 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE 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 518 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 158 ILE 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: 40.0000 chunk 259 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 chunk 298 optimal weight: 0.4980 chunk 198 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1324 ASN D 229 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS D 469 HIS D 488 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 1.0267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29224 Z= 0.207 Angle : 0.698 11.693 40154 Z= 0.352 Chirality : 0.043 0.264 4788 Planarity : 0.004 0.078 4906 Dihedral : 16.369 176.234 5048 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 3.70 % Allowed : 33.18 % Favored : 63.12 % 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: -0.78 (0.14), residues: 3587 helix: 0.80 (0.15), residues: 1295 sheet: -0.17 (0.27), residues: 378 loop : -1.58 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1276 HIS 0.013 0.001 HIS D1366 PHE 0.022 0.001 PHE C 464 TYR 0.026 0.002 TYR C1281 ARG 0.009 0.001 ARG D 297 *********************** 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 480 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 383 time to evaluate : 3.270 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: C 157 PHE cc_start: 0.4005 (m-10) cc_final: 0.2833 (m-10) REVERT: C 1290 MET cc_start: 0.6108 (ttt) cc_final: 0.5891 (ttt) REVERT: D 29 MET cc_start: 0.5556 (ttm) cc_final: 0.5227 (ttp) REVERT: D 130 MET cc_start: 0.4472 (mpp) cc_final: 0.3904 (mpp) REVERT: D 993 GLU cc_start: 0.1336 (mt-10) cc_final: 0.1004 (mt-10) REVERT: E 16 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7142 (ttm-80) REVERT: M 158 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.4383 (tt) outliers start: 97 outliers final: 66 residues processed: 449 average time/residue: 0.3487 time to fit residues: 264.2745 Evaluate side-chains 410 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 343 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 498 ILE 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 605 TYR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE 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 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 280 LYS 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: 30.0000 chunk 211 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 462 ASN C 568 ASN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 1.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29224 Z= 0.237 Angle : 0.726 14.956 40154 Z= 0.365 Chirality : 0.043 0.189 4788 Planarity : 0.005 0.095 4906 Dihedral : 16.371 176.684 5048 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 3.51 % Allowed : 33.30 % Favored : 63.19 % 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: -0.83 (0.14), residues: 3587 helix: 0.76 (0.15), residues: 1295 sheet: -0.19 (0.27), residues: 378 loop : -1.61 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 126 HIS 0.009 0.001 HIS C1070 PHE 0.033 0.002 PHE D 141 TYR 0.064 0.002 TYR C1281 ARG 0.008 0.001 ARG C 175 *********************** 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 442 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 350 time to evaluate : 3.145 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: C 124 MET cc_start: 0.5979 (tpp) cc_final: 0.5234 (tpp) REVERT: C 456 VAL cc_start: 0.8178 (p) cc_final: 0.7975 (p) REVERT: C 1230 MET cc_start: 0.8095 (tmm) cc_final: 0.7228 (ttp) REVERT: D 102 MET cc_start: 0.4914 (ttm) cc_final: 0.4539 (ttm) REVERT: D 130 MET cc_start: 0.4984 (mpp) cc_final: 0.4770 (mpp) REVERT: D 495 ASN cc_start: 0.6503 (p0) cc_final: 0.5149 (p0) REVERT: D 993 GLU cc_start: 0.2007 (mt-10) cc_final: 0.0763 (mt-10) REVERT: D 1143 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.5616 (m-30) REVERT: D 1152 GLU cc_start: 0.7334 (tp30) cc_final: 0.7113 (tp30) outliers start: 92 outliers final: 57 residues processed: 421 average time/residue: 0.3497 time to fit residues: 248.7007 Evaluate side-chains 383 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 325 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 59 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 180 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 30 ILE 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 146 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU 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 518 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 9.9990 chunk 338 optimal weight: 50.0000 chunk 309 optimal weight: 20.0000 chunk 329 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 101 optimal weight: 0.0050 chunk 297 optimal weight: 0.0010 chunk 311 optimal weight: 20.0000 chunk 328 optimal weight: 30.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 1.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 29224 Z= 0.320 Angle : 0.811 18.411 40154 Z= 0.407 Chirality : 0.046 0.236 4788 Planarity : 0.006 0.102 4906 Dihedral : 16.489 176.603 5048 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 3.63 % Allowed : 33.68 % Favored : 62.70 % 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: -0.94 (0.14), residues: 3587 helix: 0.66 (0.15), residues: 1310 sheet: -0.23 (0.28), residues: 353 loop : -1.67 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 126 HIS 0.013 0.001 HIS D1366 PHE 0.045 0.002 PHE C 828 TYR 0.030 0.002 TYR D 995 ARG 0.022 0.001 ARG C 779 *********************** 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 399 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 304 time to evaluate : 3.810 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: C 1066 MET cc_start: 0.7263 (mmm) cc_final: 0.6536 (mmm) REVERT: C 1109 ILE cc_start: 0.7081 (mm) cc_final: 0.6604 (mm) REVERT: C 1246 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7726 (ttt180) REVERT: C 1281 TYR cc_start: 0.7679 (m-80) cc_final: 0.7218 (m-80) REVERT: D 330 MET cc_start: 0.6593 (ppp) cc_final: 0.6377 (ppp) REVERT: D 698 MET cc_start: 0.7754 (mmm) cc_final: 0.7310 (tpp) REVERT: E 7 GLN cc_start: 0.6787 (tp40) cc_final: 0.6301 (tm-30) REVERT: E 26 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7499 (mmm160) outliers start: 95 outliers final: 63 residues processed: 378 average time/residue: 0.3708 time to fit residues: 233.2794 Evaluate side-chains 328 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 264 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU 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 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 239 MET 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 519 ASN Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 20.0000 chunk 348 optimal weight: 0.0170 chunk 212 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 291 optimal weight: 0.2980 chunk 30 optimal weight: 40.0000 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 1.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29224 Z= 0.220 Angle : 0.760 14.419 40154 Z= 0.377 Chirality : 0.044 0.277 4788 Planarity : 0.004 0.071 4906 Dihedral : 16.425 175.753 5048 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.09 % Rotamer: Outliers : 2.02 % Allowed : 35.97 % Favored : 62.01 % 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: -0.84 (0.14), residues: 3587 helix: 0.76 (0.15), residues: 1289 sheet: -0.24 (0.27), residues: 376 loop : -1.60 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 285 HIS 0.004 0.001 HIS A 132 PHE 0.022 0.001 PHE C 157 TYR 0.027 0.001 TYR B 152 ARG 0.011 0.001 ARG D1369 ********************** 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 341 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 288 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1230 MET cc_start: 0.8075 (tmm) cc_final: 0.7237 (ttp) REVERT: D 330 MET cc_start: 0.6304 (ppp) cc_final: 0.5931 (ppp) REVERT: D 698 MET cc_start: 0.7631 (mmm) cc_final: 0.7373 (tpp) REVERT: D 1260 MET cc_start: 0.6227 (mmm) cc_final: 0.5829 (mmm) REVERT: E 7 GLN cc_start: 0.6979 (tp40) cc_final: 0.6562 (tm-30) REVERT: E 26 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7219 (mmm160) REVERT: M 357 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.6011 (pp30) outliers start: 53 outliers final: 45 residues processed: 331 average time/residue: 0.3678 time to fit residues: 206.1234 Evaluate side-chains 311 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU 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 239 MET Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU 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 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 291 optimal weight: 20.0000 chunk 122 optimal weight: 0.0000 chunk 299 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058345 restraints weight = 129368.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060061 restraints weight = 67573.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061185 restraints weight = 44604.996| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 1.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29224 Z= 0.298 Angle : 0.793 13.810 40154 Z= 0.399 Chirality : 0.045 0.419 4788 Planarity : 0.005 0.078 4906 Dihedral : 16.483 177.016 5048 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 2.44 % Allowed : 35.47 % Favored : 62.08 % 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: -0.94 (0.14), residues: 3587 helix: 0.64 (0.15), residues: 1302 sheet: -0.38 (0.27), residues: 374 loop : -1.62 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 285 HIS 0.009 0.001 HIS D 104 PHE 0.039 0.002 PHE E 17 TYR 0.020 0.002 TYR C 605 ARG 0.027 0.001 ARG D 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6447.44 seconds wall clock time: 116 minutes 16.27 seconds (6976.27 seconds total)