Starting phenix.real_space_refine on Wed Mar 20 19:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/03_2024/6gh5_0001.pdb" } resolution = 3.4 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= 0.008 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: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 97 5.16 5 C 17442 2.51 5 N 5014 2.21 5 O 5671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C LEU 699": "CD1" <-> "CD2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 720": "NH1" <-> "NH2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1301": "NH1" <-> "NH2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28316 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2302 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1733 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10034 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 674 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 362 Chain: "D" Number of atoms: 9790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 9790 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1290} Chain breaks: 4 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 12, 'GLU:plan': 25, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 466 Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 565 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2002 Classifications: {'peptide': 338} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 192} Link IDs: {'PTRANS': 10, 'TRANS': 327} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 652 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'UNK:plan-1': 50, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 398 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 944 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 15.12, per 1000 atoms: 0.53 Number of scatterers: 28316 At special positions: 0 Unit cell: (140.98, 167.48, 160.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 92 15.00 O 5671 8.00 N 5014 7.00 C 17442 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: 12.41 Conformation dependent library (CDL) restraints added in 5.4 seconds 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 38 sheets defined 38.7% alpha, 10.7% beta 29 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 9.91 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.743A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.696A 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 157 through 162 removed outlier: 3.714A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.569A pdb=" N ASP A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.617A pdb=" N SER A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.628A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.883A pdb=" N GLU B 163 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.006A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.625A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.734A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.877A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.047A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.844A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.551A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.521A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 4.168A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.551A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 476 removed outlier: 4.053A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.031A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.593A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.821A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 656 through 660 removed outlier: 4.157A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.598A 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 686 removed outlier: 3.603A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.782A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.786A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.245A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 979 removed outlier: 3.694A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.675A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 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 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.636A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1176 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.618A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.686A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.852A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.776A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.657A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.914A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.555A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.820A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.648A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.854A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) 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 474 through 482 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.814A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 4.178A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.554A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.555A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.968A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.740A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.524A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.570A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.472A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1309 through 1315 removed outlier: 3.564A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.618A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.822A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.801A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.749A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (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 119 through 130 removed outlier: 3.524A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 removed outlier: 3.508A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.823A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.774A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 239 removed outlier: 3.915A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.118A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 355 removed outlier: 3.518A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP M 338 " --> pdb=" O GLU M 334 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU M 341 " --> pdb=" O ASN M 337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 342 " --> pdb=" O ASP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 4.156A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 Processing helix chain 'M' and resid 416 through 430 removed outlier: 3.815A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.738A pdb=" N LEU M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 9.340A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.581A 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: 3.885A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 3.581A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.902A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.155A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.882A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.979A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.621A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.229A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.359A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 722 through 726 removed outlier: 7.011A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.224A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 111 removed outlier: 6.348A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 528 removed outlier: 3.542A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 748 through 749 removed outlier: 3.525A pdb=" N SER D 753 " --> pdb=" O LYS D 749 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AD7, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AD8, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AD9, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE1, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE2, first strand: chain 'M' and resid 287 through 288 removed outlier: 5.956A pdb=" N UNK M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 13.96 Time building geometry restraints manager: 13.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.22: 776 1.22 - 1.41: 10343 1.41 - 1.60: 17155 1.60 - 1.79: 514 1.79 - 1.98: 104 Bond restraints: 28892 Sorted by residual: bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.237 1.026 0.211 1.19e-02 7.06e+03 3.14e+02 bond pdb=" C TYR C 555 " pdb=" O TYR C 555 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" C VAL C1225 " pdb=" O VAL C1225 " ideal model delta sigma weight residual 1.236 1.410 -0.175 1.01e-02 9.80e+03 2.99e+02 bond pdb=" N GLY D 333 " pdb=" CA GLY D 333 " ideal model delta sigma weight residual 1.449 1.698 -0.248 1.45e-02 4.76e+03 2.93e+02 bond pdb=" CZ ARG D 99 " pdb=" NH1 ARG D 99 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 28887 not shown) Histogram of bond angle deviations from ideal: 65.55 - 82.56: 13 82.56 - 99.56: 302 99.56 - 116.57: 20857 116.57 - 133.57: 18498 133.57 - 150.58: 21 Bond angle restraints: 39691 Sorted by residual: angle pdb=" N ASP D 462 " pdb=" CA ASP D 462 " pdb=" C ASP D 462 " ideal model delta sigma weight residual 113.02 86.00 27.02 1.49e+00 4.50e-01 3.29e+02 angle pdb=" C GLU D 765 " pdb=" N GLY D 766 " pdb=" CA GLY D 766 " ideal model delta sigma weight residual 120.64 100.22 20.42 1.26e+00 6.30e-01 2.63e+02 angle pdb=" CB ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CD1 ILE A 61 " ideal model delta sigma weight residual 113.80 79.98 33.82 2.10e+00 2.27e-01 2.59e+02 angle pdb=" CG MET C 805 " pdb=" SD MET C 805 " pdb=" CE MET C 805 " ideal model delta sigma weight residual 100.90 65.55 35.35 2.20e+00 2.07e-01 2.58e+02 angle pdb=" N ASP M 186 " pdb=" CA ASP M 186 " pdb=" CB ASP M 186 " ideal model delta sigma weight residual 110.42 129.15 -18.73 1.18e+00 7.18e-01 2.52e+02 ... (remaining 39686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 16658 35.30 - 70.60: 638 70.60 - 105.90: 26 105.90 - 141.20: 3 141.20 - 176.50: 7 Dihedral angle restraints: 17332 sinusoidal: 6857 harmonic: 10475 Sorted by residual: dihedral pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual 122.80 159.58 -36.78 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C TYR C 555 " pdb=" N TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual -122.60 -159.21 36.61 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CA GLU D 534 " pdb=" CB GLU D 534 " ideal model delta harmonic sigma weight residual 122.80 159.04 -36.24 0 2.50e+00 1.60e-01 2.10e+02 ... (remaining 17329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 4665 0.615 - 1.230: 98 1.230 - 1.844: 10 1.844 - 2.459: 0 2.459 - 3.074: 1 Chirality restraints: 4774 Sorted by residual: chirality pdb=" CG LEU C 699 " pdb=" CB LEU C 699 " pdb=" CD1 LEU C 699 " pdb=" CD2 LEU C 699 " both_signs ideal model delta sigma weight residual False -2.59 0.48 -3.07 2.00e-01 2.50e+01 2.36e+02 chirality pdb=" CA GLU D 534 " pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CB GLU D 534 " both_signs ideal model delta sigma weight residual False 2.51 0.87 1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" CA TYR C 555 " pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CB TYR C 555 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.67e+01 ... (remaining 4771 not shown) Planarity restraints: 4889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " 0.018 2.00e-02 2.50e+03 1.06e-01 2.80e+02 pdb=" CG TRP C1276 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.111 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.127 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.065 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 380 " -0.071 2.00e-02 2.50e+03 1.10e-01 2.11e+02 pdb=" CG PHE D 380 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 PHE D 380 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 380 " 0.104 2.00e-02 2.50e+03 pdb=" CE1 PHE D 380 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE D 380 " -0.191 2.00e-02 2.50e+03 pdb=" CZ PHE D 380 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.128 2.00e-02 2.50e+03 7.03e-02 1.23e+02 pdb=" CG TRP D 115 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.116 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.077 2.00e-02 2.50e+03 ... (remaining 4886 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 177 2.46 - 3.07: 19488 3.07 - 3.68: 41568 3.68 - 4.29: 62237 4.29 - 4.90: 96609 Nonbonded interactions: 220079 Sorted by model distance: nonbonded pdb=" CD1 ILE D 316 " pdb=" N THR D 317 " model vdw 1.847 3.540 nonbonded pdb=" O GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.882 2.520 nonbonded pdb=" CA GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.994 3.520 nonbonded pdb=" O HIS D 113 " pdb=" CB HIS D 113 " model vdw 2.030 2.752 nonbonded pdb=" CD1 ILE D 316 " pdb=" O THR D 317 " model vdw 2.049 3.460 ... (remaining 220074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.010 Extract box with map and model: 5.200 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 84.290 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.033 0.383 28892 Z= 2.221 Angle : 3.297 39.068 39691 Z= 1.968 Chirality : 0.221 3.074 4774 Planarity : 0.019 0.160 4889 Dihedral : 17.386 176.499 10564 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 2.30 % Allowed : 11.02 % Favored : 86.68 % Rotamer: Outliers : 4.29 % Allowed : 8.51 % Favored : 87.20 % Cbeta Deviations : 9.84 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.55 % 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: -4.34 (0.11), residues: 3567 helix: -3.21 (0.10), residues: 1267 sheet: -1.73 (0.27), residues: 316 loop : -2.91 (0.11), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.181 0.030 TRP C1276 HIS 0.103 0.017 HIS C1116 PHE 0.191 0.024 PHE D 380 TYR 0.125 0.022 TYR D 899 ARG 0.160 0.008 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 615 time to evaluate : 2.496 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: A 147 GLN cc_start: 0.9315 (pt0) cc_final: 0.8782 (pt0) REVERT: A 201 LEU cc_start: 0.9423 (tp) cc_final: 0.9201 (tt) REVERT: B 18 GLN cc_start: 0.9418 (pm20) cc_final: 0.9113 (pm20) REVERT: B 51 MET cc_start: 0.9284 (tpp) cc_final: 0.9033 (mmm) REVERT: B 125 LYS cc_start: 0.9340 (pttt) cc_final: 0.9092 (pttp) REVERT: C 5 TYR cc_start: 0.8403 (m-80) cc_final: 0.7951 (m-10) REVERT: C 80 PHE cc_start: 0.9296 (m-10) cc_final: 0.9010 (m-10) REVERT: C 88 ARG cc_start: 0.9238 (mtt180) cc_final: 0.7678 (tpt-90) REVERT: C 149 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9173 (tp) REVERT: C 165 HIS cc_start: 0.9116 (t70) cc_final: 0.8541 (t-90) REVERT: C 369 MET cc_start: 0.8967 (tpt) cc_final: 0.8688 (tpp) REVERT: C 370 MET cc_start: 0.8603 (mmm) cc_final: 0.8313 (mmm) REVERT: C 464 PHE cc_start: 0.9513 (t80) cc_final: 0.9213 (t80) REVERT: C 564 PRO cc_start: 0.9677 (OUTLIER) cc_final: 0.9426 (Cg_endo) REVERT: C 603 ILE cc_start: 0.9706 (pt) cc_final: 0.9421 (mm) REVERT: C 696 ASP cc_start: 0.9371 (t0) cc_final: 0.9062 (t0) REVERT: C 697 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9037 (ptpp) REVERT: C 765 ILE cc_start: 0.9259 (pp) cc_final: 0.8919 (mp) REVERT: C 821 ARG cc_start: 0.9518 (OUTLIER) cc_final: 0.9251 (tpp80) REVERT: C 929 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9322 (tt) REVERT: C 1029 LEU cc_start: 0.9124 (tt) cc_final: 0.8897 (tt) REVERT: C 1030 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9239 (tp30) REVERT: C 1050 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9066 (t) REVERT: C 1268 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9038 (mm-40) REVERT: C 1290 MET cc_start: 0.9765 (mmt) cc_final: 0.9439 (mmt) REVERT: C 1319 MET cc_start: 0.9538 (OUTLIER) cc_final: 0.9309 (tpp) REVERT: D 15 GLU cc_start: 0.9149 (pt0) cc_final: 0.8787 (pm20) REVERT: D 43 THR cc_start: 0.9378 (p) cc_final: 0.9133 (p) REVERT: D 68 TYR cc_start: 0.9474 (m-80) cc_final: 0.9230 (m-80) REVERT: D 80 HIS cc_start: 0.8012 (p90) cc_final: 0.7534 (p90) REVERT: D 93 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9037 (t) REVERT: D 192 MET cc_start: 0.9447 (tpp) cc_final: 0.9244 (tpp) REVERT: D 253 VAL cc_start: 0.9417 (m) cc_final: 0.9092 (p) REVERT: D 262 THR cc_start: 0.9234 (m) cc_final: 0.9012 (t) REVERT: D 339 ARG cc_start: 0.9436 (tpp-160) cc_final: 0.9061 (ttm170) REVERT: D 394 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9466 (tp) REVERT: D 462 ASP cc_start: 0.8994 (p0) cc_final: 0.7998 (p0) REVERT: D 490 ILE cc_start: 0.9389 (pt) cc_final: 0.8813 (mt) REVERT: D 605 LEU cc_start: 0.9758 (mt) cc_final: 0.9556 (mm) REVERT: D 619 ILE cc_start: 0.9098 (tt) cc_final: 0.8672 (pt) REVERT: D 625 MET cc_start: 0.9664 (ttp) cc_final: 0.9458 (ttp) REVERT: D 644 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9298 (mpp) REVERT: D 668 PHE cc_start: 0.7898 (t80) cc_final: 0.7581 (t80) REVERT: D 716 GLN cc_start: 0.8512 (tt0) cc_final: 0.8247 (pt0) REVERT: D 719 PHE cc_start: 0.7660 (m-80) cc_final: 0.7170 (m-80) REVERT: D 826 ILE cc_start: 0.9349 (pt) cc_final: 0.8887 (mt) REVERT: D 833 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8914 (mt-10) REVERT: D 848 VAL cc_start: 0.9348 (m) cc_final: 0.8947 (p) REVERT: D 1040 MET cc_start: 0.8273 (mtp) cc_final: 0.7876 (mmm) REVERT: D 1250 ASP cc_start: 0.9465 (m-30) cc_final: 0.9144 (m-30) REVERT: D 1263 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.8989 (mmmt) REVERT: D 1325 PHE cc_start: 0.9386 (t80) cc_final: 0.9080 (t80) REVERT: E 30 MET cc_start: 0.9213 (mtm) cc_final: 0.8898 (mtp) REVERT: E 41 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9322 (tt0) REVERT: E 42 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9193 (mp0) REVERT: E 44 ASP cc_start: 0.9230 (p0) cc_final: 0.8965 (p0) REVERT: E 71 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9154 (pp20) REVERT: M 121 GLN cc_start: 0.9553 (mp10) cc_final: 0.9257 (mt0) REVERT: M 137 ASP cc_start: 0.9387 (m-30) cc_final: 0.8808 (t70) REVERT: M 376 MET cc_start: 0.5984 (mmm) cc_final: 0.4501 (tpp) outliers start: 111 outliers final: 27 residues processed: 697 average time/residue: 0.4374 time to fit residues: 464.4806 Evaluate side-chains 381 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 342 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 564 PRO Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 821 ARG Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 1263 LYS Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain M residue 156 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 132 HIS B 132 HIS C 165 HIS C 193 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 554 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 799 ASN C 856 ASN C1080 ASN C1116 HIS C1136 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN D 157 GLN D 435 GLN D 560 ASN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D1249 ASN D1259 GLN M 127 GLN M 157 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28892 Z= 0.293 Angle : 0.834 15.579 39691 Z= 0.434 Chirality : 0.047 0.287 4774 Planarity : 0.006 0.127 4889 Dihedral : 18.135 177.349 4964 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 1.07 % Allowed : 7.93 % Favored : 91.00 % Rotamer: Outliers : 3.44 % Allowed : 13.19 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.12), residues: 3567 helix: -1.04 (0.13), residues: 1277 sheet: -1.01 (0.28), residues: 288 loop : -2.48 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 115 HIS 0.007 0.001 HIS C 673 PHE 0.019 0.002 PHE D 461 TYR 0.024 0.002 TYR B 185 ARG 0.013 0.001 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 360 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.9437 (pm20) cc_final: 0.9099 (pm20) REVERT: B 125 LYS cc_start: 0.9223 (pttt) cc_final: 0.9017 (pttp) REVERT: C 80 PHE cc_start: 0.9306 (m-10) cc_final: 0.8887 (m-80) REVERT: C 88 ARG cc_start: 0.9244 (mtt180) cc_final: 0.7999 (ttt-90) REVERT: C 141 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8393 (m) REVERT: C 165 HIS cc_start: 0.9141 (t-90) cc_final: 0.8524 (t-90) REVERT: C 316 GLU cc_start: 0.8905 (mp0) cc_final: 0.8491 (mm-30) REVERT: C 603 ILE cc_start: 0.9727 (pt) cc_final: 0.9458 (mm) REVERT: C 699 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8908 (tp) REVERT: C 918 LEU cc_start: 0.9620 (tp) cc_final: 0.9412 (tp) REVERT: C 949 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (mp0) REVERT: C 1030 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9266 (tp30) REVERT: C 1161 LEU cc_start: 0.9343 (mp) cc_final: 0.9128 (mt) REVERT: D 15 GLU cc_start: 0.8969 (pt0) cc_final: 0.8521 (tm-30) REVERT: D 43 THR cc_start: 0.9242 (p) cc_final: 0.8947 (p) REVERT: D 80 HIS cc_start: 0.7672 (p90) cc_final: 0.7336 (p90) REVERT: D 93 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8998 (t) REVERT: D 113 HIS cc_start: 0.8614 (t-170) cc_final: 0.7767 (t70) REVERT: D 130 MET cc_start: 0.9463 (mtt) cc_final: 0.9092 (ttm) REVERT: D 339 ARG cc_start: 0.9210 (tpp-160) cc_final: 0.8757 (mtt180) REVERT: D 490 ILE cc_start: 0.9359 (pt) cc_final: 0.8660 (mt) REVERT: D 619 ILE cc_start: 0.9069 (tt) cc_final: 0.8774 (pt) REVERT: D 625 MET cc_start: 0.9567 (ttp) cc_final: 0.9328 (ttp) REVERT: D 803 VAL cc_start: 0.9323 (t) cc_final: 0.8686 (p) REVERT: D 807 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8980 (mt) REVERT: D 826 ILE cc_start: 0.9222 (pt) cc_final: 0.8713 (mt) REVERT: D 848 VAL cc_start: 0.9238 (m) cc_final: 0.8803 (p) REVERT: D 987 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: D 1040 MET cc_start: 0.8332 (mtp) cc_final: 0.7918 (mmm) REVERT: E 3 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8884 (mmm-85) REVERT: E 42 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9083 (mp0) REVERT: M 137 ASP cc_start: 0.9448 (m-30) cc_final: 0.8945 (t0) REVERT: M 149 ASP cc_start: 0.8790 (m-30) cc_final: 0.8526 (p0) REVERT: M 376 MET cc_start: 0.6244 (mmm) cc_final: 0.5292 (mmm) outliers start: 89 outliers final: 31 residues processed: 429 average time/residue: 0.4014 time to fit residues: 273.2440 Evaluate side-chains 325 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 288 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 228 optimal weight: 0.0770 chunk 92 optimal weight: 8.9990 chunk 335 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C1257 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28892 Z= 0.305 Angle : 0.751 15.432 39691 Z= 0.389 Chirality : 0.045 0.236 4774 Planarity : 0.005 0.080 4889 Dihedral : 17.862 179.037 4892 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.97 % Favored : 90.02 % Rotamer: Outliers : 3.13 % Allowed : 15.24 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % 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: -1.85 (0.13), residues: 3567 helix: 0.01 (0.14), residues: 1283 sheet: -0.73 (0.28), residues: 302 loop : -2.25 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 321 HIS 0.007 0.001 HIS D 80 PHE 0.015 0.002 PHE D 620 TYR 0.023 0.002 TYR C 123 ARG 0.011 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 312 time to evaluate : 2.889 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: A 158 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8308 (ttp80) REVERT: B 18 GLN cc_start: 0.9512 (pm20) cc_final: 0.9225 (pm20) REVERT: C 80 PHE cc_start: 0.9347 (m-10) cc_final: 0.8971 (m-80) REVERT: C 88 ARG cc_start: 0.9335 (mtt180) cc_final: 0.8785 (ttm110) REVERT: C 165 HIS cc_start: 0.9151 (t-90) cc_final: 0.8523 (t-90) REVERT: C 316 GLU cc_start: 0.8957 (mp0) cc_final: 0.8486 (tp30) REVERT: C 369 MET cc_start: 0.8902 (tpt) cc_final: 0.8686 (tpt) REVERT: C 370 MET cc_start: 0.8679 (tpt) cc_final: 0.8389 (tpt) REVERT: C 471 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9017 (p) REVERT: C 603 ILE cc_start: 0.9722 (pt) cc_final: 0.9445 (mm) REVERT: C 704 MET cc_start: 0.8738 (mtp) cc_final: 0.8490 (mtp) REVERT: D 15 GLU cc_start: 0.8941 (pt0) cc_final: 0.8493 (tm-30) REVERT: D 80 HIS cc_start: 0.7663 (p90) cc_final: 0.7106 (p90) REVERT: D 83 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8086 (t) REVERT: D 96 LYS cc_start: 0.8676 (pttm) cc_final: 0.8263 (mppt) REVERT: D 113 HIS cc_start: 0.8724 (t-170) cc_final: 0.7911 (t70) REVERT: D 117 LEU cc_start: 0.8751 (tt) cc_final: 0.8475 (tp) REVERT: D 130 MET cc_start: 0.9478 (mtt) cc_final: 0.9112 (ttm) REVERT: D 485 MET cc_start: 0.9212 (mmt) cc_final: 0.9003 (mmt) REVERT: D 490 ILE cc_start: 0.9358 (pt) cc_final: 0.8828 (mt) REVERT: D 619 ILE cc_start: 0.9075 (tt) cc_final: 0.8803 (pt) REVERT: D 716 GLN cc_start: 0.8508 (tt0) cc_final: 0.8250 (tt0) REVERT: D 803 VAL cc_start: 0.9415 (t) cc_final: 0.8690 (p) REVERT: D 807 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8998 (mt) REVERT: D 826 ILE cc_start: 0.9249 (pt) cc_final: 0.8730 (mt) REVERT: D 848 VAL cc_start: 0.9257 (m) cc_final: 0.8844 (p) REVERT: D 981 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8465 (pm20) REVERT: D 1040 MET cc_start: 0.8413 (mtp) cc_final: 0.8009 (mmm) REVERT: E 3 ARG cc_start: 0.9242 (mmm160) cc_final: 0.9013 (mmm-85) REVERT: M 376 MET cc_start: 0.6249 (mmm) cc_final: 0.5378 (mmm) outliers start: 81 outliers final: 38 residues processed: 376 average time/residue: 0.3928 time to fit residues: 235.8543 Evaluate side-chains 315 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 274 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 176 optimal weight: 0.3980 chunk 319 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 447 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28892 Z= 0.239 Angle : 0.701 15.069 39691 Z= 0.360 Chirality : 0.043 0.335 4774 Planarity : 0.004 0.078 4889 Dihedral : 17.658 178.014 4889 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.61 % Favored : 90.38 % Rotamer: Outliers : 3.02 % Allowed : 16.78 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % 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: -1.45 (0.14), residues: 3567 helix: 0.58 (0.15), residues: 1274 sheet: -0.57 (0.28), residues: 307 loop : -2.18 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 321 HIS 0.005 0.001 HIS D 80 PHE 0.015 0.001 PHE D 57 TYR 0.016 0.001 TYR C 123 ARG 0.009 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 289 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.9568 (pm20) cc_final: 0.9157 (pm20) REVERT: B 125 LYS cc_start: 0.8865 (pttp) cc_final: 0.8427 (pptt) REVERT: C 165 HIS cc_start: 0.9199 (t-90) cc_final: 0.8602 (t-90) REVERT: C 187 GLU cc_start: 0.9346 (tt0) cc_final: 0.9017 (tm-30) REVERT: C 316 GLU cc_start: 0.8968 (mp0) cc_final: 0.8563 (mm-30) REVERT: C 369 MET cc_start: 0.8935 (tpt) cc_final: 0.8639 (tpt) REVERT: C 370 MET cc_start: 0.8776 (tpt) cc_final: 0.8530 (tpt) REVERT: C 471 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8982 (p) REVERT: C 548 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8447 (mmt180) REVERT: C 603 ILE cc_start: 0.9713 (pt) cc_final: 0.9439 (mm) REVERT: C 704 MET cc_start: 0.8787 (mtp) cc_final: 0.8573 (mtp) REVERT: C 754 THR cc_start: 0.9145 (p) cc_final: 0.8934 (t) REVERT: D 15 GLU cc_start: 0.8917 (pt0) cc_final: 0.8419 (tm-30) REVERT: D 80 HIS cc_start: 0.7500 (p90) cc_final: 0.6965 (p90) REVERT: D 83 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8153 (t) REVERT: D 96 LYS cc_start: 0.8621 (pttm) cc_final: 0.8187 (mppt) REVERT: D 113 HIS cc_start: 0.8619 (t-170) cc_final: 0.7642 (t70) REVERT: D 117 LEU cc_start: 0.8653 (tt) cc_final: 0.8379 (tp) REVERT: D 130 MET cc_start: 0.9512 (mtt) cc_final: 0.9170 (ttm) REVERT: D 339 ARG cc_start: 0.9224 (tpp-160) cc_final: 0.8597 (mtt180) REVERT: D 490 ILE cc_start: 0.9287 (pt) cc_final: 0.8764 (mt) REVERT: D 619 ILE cc_start: 0.9089 (tt) cc_final: 0.8811 (pt) REVERT: D 807 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9012 (mt) REVERT: D 826 ILE cc_start: 0.9245 (pt) cc_final: 0.8712 (mt) REVERT: D 848 VAL cc_start: 0.9298 (m) cc_final: 0.8922 (p) REVERT: D 981 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8373 (pm20) REVERT: D 987 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: D 1040 MET cc_start: 0.8435 (mtp) cc_final: 0.8042 (mmm) REVERT: E 3 ARG cc_start: 0.9228 (mmm160) cc_final: 0.8999 (mmm-85) REVERT: E 41 GLU cc_start: 0.9441 (tt0) cc_final: 0.9168 (tm-30) REVERT: M 181 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8570 (mmm-85) REVERT: M 376 MET cc_start: 0.6299 (mmm) cc_final: 0.5456 (mmm) outliers start: 78 outliers final: 48 residues processed: 352 average time/residue: 0.3951 time to fit residues: 223.8788 Evaluate side-chains 325 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 908 ILE Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS D 739 GLN D 861 ASN D1279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 28892 Z= 0.431 Angle : 0.763 16.097 39691 Z= 0.394 Chirality : 0.046 0.286 4774 Planarity : 0.005 0.082 4889 Dihedral : 17.666 179.324 4887 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.22 % Favored : 89.71 % Rotamer: Outliers : 3.67 % Allowed : 17.94 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -1.36 (0.14), residues: 3567 helix: 0.68 (0.15), residues: 1277 sheet: -0.48 (0.29), residues: 304 loop : -2.15 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.008 0.001 HIS D 80 PHE 0.021 0.002 PHE D1325 TYR 0.022 0.002 TYR C 123 ARG 0.008 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 270 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8664 (mpt180) REVERT: A 307 LEU cc_start: 0.9420 (tp) cc_final: 0.9093 (tp) REVERT: B 18 GLN cc_start: 0.9559 (pm20) cc_final: 0.9327 (pm20) REVERT: C 165 HIS cc_start: 0.9202 (t-90) cc_final: 0.8578 (t-90) REVERT: C 187 GLU cc_start: 0.9315 (tt0) cc_final: 0.9042 (tm-30) REVERT: C 195 PHE cc_start: 0.8488 (m-80) cc_final: 0.8273 (m-10) REVERT: C 316 GLU cc_start: 0.9005 (mp0) cc_final: 0.8599 (tp30) REVERT: C 369 MET cc_start: 0.8962 (tpt) cc_final: 0.8654 (tpt) REVERT: C 471 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8991 (p) REVERT: C 548 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8400 (mmt180) REVERT: C 603 ILE cc_start: 0.9698 (pt) cc_final: 0.9384 (mt) REVERT: D 15 GLU cc_start: 0.8997 (pt0) cc_final: 0.8522 (tm-30) REVERT: D 80 HIS cc_start: 0.7580 (p90) cc_final: 0.7284 (p90) REVERT: D 83 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8101 (p) REVERT: D 96 LYS cc_start: 0.8699 (pttm) cc_final: 0.8227 (mppt) REVERT: D 113 HIS cc_start: 0.8872 (t-170) cc_final: 0.8073 (t70) REVERT: D 117 LEU cc_start: 0.8753 (tt) cc_final: 0.8463 (tp) REVERT: D 130 MET cc_start: 0.9531 (mtt) cc_final: 0.9114 (ttt) REVERT: D 339 ARG cc_start: 0.9280 (tpp-160) cc_final: 0.8733 (mtt180) REVERT: D 490 ILE cc_start: 0.9335 (pt) cc_final: 0.8855 (mt) REVERT: D 619 ILE cc_start: 0.9122 (tt) cc_final: 0.8922 (pt) REVERT: D 625 MET cc_start: 0.9592 (ttp) cc_final: 0.9249 (ttp) REVERT: D 807 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8945 (mt) REVERT: D 822 MET cc_start: 0.9197 (mmm) cc_final: 0.8936 (mmm) REVERT: D 826 ILE cc_start: 0.9261 (pt) cc_final: 0.8776 (mt) REVERT: D 987 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8672 (pm20) REVERT: E 3 ARG cc_start: 0.9246 (mmm160) cc_final: 0.9039 (mmm-85) REVERT: E 41 GLU cc_start: 0.9312 (tt0) cc_final: 0.9067 (tm-30) REVERT: M 376 MET cc_start: 0.6038 (mmm) cc_final: 0.5171 (mmm) outliers start: 95 outliers final: 63 residues processed: 347 average time/residue: 0.3926 time to fit residues: 219.1092 Evaluate side-chains 322 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 357 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 chunk 165 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28892 Z= 0.257 Angle : 0.698 15.067 39691 Z= 0.357 Chirality : 0.043 0.253 4774 Planarity : 0.004 0.082 4889 Dihedral : 17.556 178.136 4887 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.36 % Rotamer: Outliers : 3.67 % Allowed : 18.17 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3567 helix: 0.90 (0.15), residues: 1282 sheet: -0.40 (0.30), residues: 297 loop : -2.10 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 321 HIS 0.005 0.001 HIS D 80 PHE 0.013 0.001 PHE D 57 TYR 0.015 0.001 TYR C 123 ARG 0.008 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 274 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8697 (mmt-90) REVERT: A 307 LEU cc_start: 0.9436 (tp) cc_final: 0.9099 (tp) REVERT: B 18 GLN cc_start: 0.9565 (pm20) cc_final: 0.9270 (pm20) REVERT: B 125 LYS cc_start: 0.8723 (pttp) cc_final: 0.8391 (pptt) REVERT: C 165 HIS cc_start: 0.9129 (t-90) cc_final: 0.8658 (t70) REVERT: C 187 GLU cc_start: 0.9341 (tt0) cc_final: 0.9081 (tm-30) REVERT: C 316 GLU cc_start: 0.8997 (mp0) cc_final: 0.8569 (tp30) REVERT: C 471 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8954 (p) REVERT: C 548 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8549 (mtt180) REVERT: C 603 ILE cc_start: 0.9702 (pt) cc_final: 0.9406 (mt) REVERT: C 1231 TYR cc_start: 0.9549 (t80) cc_final: 0.9339 (t80) REVERT: D 15 GLU cc_start: 0.8939 (pt0) cc_final: 0.8464 (tm-30) REVERT: D 80 HIS cc_start: 0.7434 (p90) cc_final: 0.6963 (p90) REVERT: D 113 HIS cc_start: 0.8810 (t-170) cc_final: 0.8021 (t70) REVERT: D 117 LEU cc_start: 0.8689 (tt) cc_final: 0.8366 (tp) REVERT: D 339 ARG cc_start: 0.9239 (tpp-160) cc_final: 0.8623 (mtt180) REVERT: D 551 ARG cc_start: 0.9569 (OUTLIER) cc_final: 0.9147 (ptp-170) REVERT: D 619 ILE cc_start: 0.9087 (tt) cc_final: 0.8848 (pt) REVERT: D 706 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8079 (t) REVERT: D 807 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8944 (mt) REVERT: D 822 MET cc_start: 0.9267 (mmm) cc_final: 0.8865 (mmm) REVERT: D 826 ILE cc_start: 0.9304 (pt) cc_final: 0.8923 (mt) REVERT: D 987 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: D 1040 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8337 (mmm) REVERT: E 3 ARG cc_start: 0.9249 (mmm160) cc_final: 0.9045 (mmm-85) REVERT: E 41 GLU cc_start: 0.9303 (tt0) cc_final: 0.9044 (tm-30) REVERT: M 376 MET cc_start: 0.5997 (mmm) cc_final: 0.5142 (mmm) outliers start: 95 outliers final: 59 residues processed: 351 average time/residue: 0.4117 time to fit residues: 234.0780 Evaluate side-chains 320 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 203 optimal weight: 0.0570 chunk 260 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 300 optimal weight: 40.0000 chunk 199 optimal weight: 1.9990 chunk 355 optimal weight: 50.0000 chunk 222 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28892 Z= 0.242 Angle : 0.691 15.882 39691 Z= 0.352 Chirality : 0.043 0.219 4774 Planarity : 0.004 0.082 4889 Dihedral : 17.478 177.579 4887 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.14 % Favored : 89.94 % Rotamer: Outliers : 3.33 % Allowed : 18.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3567 helix: 1.06 (0.15), residues: 1284 sheet: -0.36 (0.30), residues: 299 loop : -2.07 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 321 HIS 0.004 0.001 HIS D 430 PHE 0.016 0.001 PHE C 80 TYR 0.014 0.001 TYR C 123 ARG 0.007 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 262 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8698 (mmt-90) REVERT: A 307 LEU cc_start: 0.9441 (tp) cc_final: 0.9072 (tp) REVERT: B 18 GLN cc_start: 0.9555 (pm20) cc_final: 0.9271 (pm20) REVERT: B 125 LYS cc_start: 0.8769 (pttp) cc_final: 0.8361 (pptt) REVERT: C 26 TYR cc_start: 0.9239 (t80) cc_final: 0.8959 (t80) REVERT: C 165 HIS cc_start: 0.9133 (t-90) cc_final: 0.8647 (t70) REVERT: C 187 GLU cc_start: 0.9325 (tt0) cc_final: 0.9010 (tm-30) REVERT: C 316 GLU cc_start: 0.8990 (mp0) cc_final: 0.8555 (tp30) REVERT: C 471 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 548 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8365 (mmt180) REVERT: C 603 ILE cc_start: 0.9700 (pt) cc_final: 0.9406 (mt) REVERT: D 15 GLU cc_start: 0.8956 (pt0) cc_final: 0.8477 (tm-30) REVERT: D 80 HIS cc_start: 0.7627 (p90) cc_final: 0.7399 (m90) REVERT: D 96 LYS cc_start: 0.8670 (pttm) cc_final: 0.8175 (mppt) REVERT: D 113 HIS cc_start: 0.8807 (t-170) cc_final: 0.7937 (t70) REVERT: D 117 LEU cc_start: 0.8712 (tt) cc_final: 0.8422 (tp) REVERT: D 130 MET cc_start: 0.9559 (mtt) cc_final: 0.9209 (ttm) REVERT: D 339 ARG cc_start: 0.9233 (tpp-160) cc_final: 0.8608 (mtt180) REVERT: D 619 ILE cc_start: 0.9084 (tt) cc_final: 0.8820 (pt) REVERT: D 706 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8067 (t) REVERT: D 807 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8990 (mt) REVERT: D 826 ILE cc_start: 0.9293 (pt) cc_final: 0.8881 (mt) REVERT: D 987 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: D 1040 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8311 (mmt) REVERT: E 3 ARG cc_start: 0.9260 (mmm160) cc_final: 0.9058 (mmm-85) REVERT: E 41 GLU cc_start: 0.9308 (tt0) cc_final: 0.9053 (tm-30) REVERT: M 181 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8843 (mmm-85) REVERT: M 376 MET cc_start: 0.5929 (mmm) cc_final: 0.4851 (mmm) outliers start: 86 outliers final: 61 residues processed: 331 average time/residue: 0.4031 time to fit residues: 214.2858 Evaluate side-chains 314 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 913 GLU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN C 526 HIS ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28892 Z= 0.381 Angle : 0.746 15.825 39691 Z= 0.381 Chirality : 0.045 0.267 4774 Planarity : 0.005 0.081 4889 Dihedral : 17.520 178.109 4887 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.64 % Favored : 89.35 % Rotamer: Outliers : 3.21 % Allowed : 19.45 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -1.12 (0.14), residues: 3567 helix: 0.97 (0.15), residues: 1295 sheet: -0.41 (0.30), residues: 299 loop : -2.10 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.006 0.001 HIS D 80 PHE 0.017 0.002 PHE D1325 TYR 0.016 0.002 TYR C 123 ARG 0.014 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 254 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8626 (mmt180) REVERT: A 307 LEU cc_start: 0.9439 (tp) cc_final: 0.9059 (tp) REVERT: B 18 GLN cc_start: 0.9545 (pm20) cc_final: 0.9281 (pm20) REVERT: B 125 LYS cc_start: 0.8779 (pttp) cc_final: 0.8358 (pptt) REVERT: C 165 HIS cc_start: 0.9137 (t-90) cc_final: 0.8629 (t70) REVERT: C 187 GLU cc_start: 0.9312 (tt0) cc_final: 0.8993 (tm-30) REVERT: C 316 GLU cc_start: 0.9033 (mp0) cc_final: 0.8622 (tp30) REVERT: C 369 MET cc_start: 0.8993 (tpt) cc_final: 0.8749 (tpt) REVERT: C 471 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 548 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8404 (mmt180) REVERT: C 603 ILE cc_start: 0.9683 (pt) cc_final: 0.9379 (mt) REVERT: C 966 ILE cc_start: 0.7756 (mt) cc_final: 0.7394 (tp) REVERT: D 15 GLU cc_start: 0.9037 (pt0) cc_final: 0.8573 (tm-30) REVERT: D 113 HIS cc_start: 0.8926 (t-170) cc_final: 0.8177 (t70) REVERT: D 117 LEU cc_start: 0.8703 (tt) cc_final: 0.8413 (tp) REVERT: D 130 MET cc_start: 0.9556 (mtt) cc_final: 0.9223 (ttm) REVERT: D 339 ARG cc_start: 0.9292 (tpp-160) cc_final: 0.8715 (mtt180) REVERT: D 619 ILE cc_start: 0.9104 (tt) cc_final: 0.8892 (pt) REVERT: D 625 MET cc_start: 0.9564 (ttp) cc_final: 0.9168 (ttp) REVERT: D 706 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8103 (t) REVERT: D 807 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8938 (mt) REVERT: D 822 MET cc_start: 0.9079 (mmm) cc_final: 0.8806 (mmm) REVERT: D 826 ILE cc_start: 0.9283 (pt) cc_final: 0.8896 (mt) REVERT: D 1040 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: E 41 GLU cc_start: 0.9285 (tt0) cc_final: 0.9045 (tm-30) REVERT: M 181 ARG cc_start: 0.9178 (mtp180) cc_final: 0.8794 (mmm-85) REVERT: M 376 MET cc_start: 0.5729 (mmm) cc_final: 0.4598 (mmp) outliers start: 83 outliers final: 70 residues processed: 316 average time/residue: 0.4193 time to fit residues: 216.8518 Evaluate side-chains 322 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 247 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 958 ILE Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 299 optimal weight: 9.9990 chunk 313 optimal weight: 7.9990 chunk 330 optimal weight: 0.6980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN C 554 HIS ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 72 GLN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28892 Z= 0.371 Angle : 0.746 15.390 39691 Z= 0.381 Chirality : 0.045 0.257 4774 Planarity : 0.005 0.084 4889 Dihedral : 17.511 178.400 4887 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.81 % Favored : 89.23 % Rotamer: Outliers : 3.09 % Allowed : 19.76 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % 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: -1.10 (0.14), residues: 3567 helix: 1.01 (0.15), residues: 1299 sheet: -0.51 (0.29), residues: 316 loop : -2.10 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 321 HIS 0.006 0.001 HIS D 113 PHE 0.044 0.002 PHE C 514 TYR 0.015 0.002 TYR C 123 ARG 0.007 0.001 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 252 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.9405 (tp) cc_final: 0.9016 (tp) REVERT: B 18 GLN cc_start: 0.9519 (pm20) cc_final: 0.9266 (pm20) REVERT: B 125 LYS cc_start: 0.8730 (pttp) cc_final: 0.8290 (pptt) REVERT: C 165 HIS cc_start: 0.9134 (t-90) cc_final: 0.8638 (t70) REVERT: C 316 GLU cc_start: 0.9032 (mp0) cc_final: 0.8659 (tp30) REVERT: C 369 MET cc_start: 0.8999 (tpt) cc_final: 0.8746 (tpt) REVERT: C 471 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 548 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8372 (mmt180) REVERT: C 603 ILE cc_start: 0.9700 (pt) cc_final: 0.9396 (mt) REVERT: C 966 ILE cc_start: 0.7740 (mt) cc_final: 0.7449 (tp) REVERT: D 15 GLU cc_start: 0.9073 (pt0) cc_final: 0.8642 (tm-30) REVERT: D 117 LEU cc_start: 0.8662 (tt) cc_final: 0.8355 (tp) REVERT: D 339 ARG cc_start: 0.9289 (tpp-160) cc_final: 0.8717 (mtt180) REVERT: D 625 MET cc_start: 0.9549 (ttp) cc_final: 0.9117 (ttp) REVERT: D 706 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8215 (t) REVERT: D 807 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8864 (mt) REVERT: D 822 MET cc_start: 0.8991 (mmm) cc_final: 0.8695 (mmm) REVERT: D 826 ILE cc_start: 0.9293 (pt) cc_final: 0.8895 (mt) REVERT: D 1040 MET cc_start: 0.8768 (mtt) cc_final: 0.8399 (mmt) REVERT: D 1159 ILE cc_start: 0.5123 (OUTLIER) cc_final: 0.4907 (mm) REVERT: E 41 GLU cc_start: 0.9257 (tt0) cc_final: 0.9024 (tm-30) REVERT: M 181 ARG cc_start: 0.9190 (mtp180) cc_final: 0.8775 (mmm160) REVERT: M 376 MET cc_start: 0.5694 (mmm) cc_final: 0.4608 (mmp) outliers start: 80 outliers final: 68 residues processed: 313 average time/residue: 0.3817 time to fit residues: 195.4780 Evaluate side-chains 315 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 242 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 0.9990 chunk 350 optimal weight: 40.0000 chunk 213 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 0.7980 chunk 292 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN E 43 ASN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28892 Z= 0.266 Angle : 0.716 15.097 39691 Z= 0.362 Chirality : 0.043 0.253 4774 Planarity : 0.004 0.083 4889 Dihedral : 17.442 178.630 4887 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.94 % Favored : 90.05 % Rotamer: Outliers : 2.86 % Allowed : 20.15 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3567 helix: 1.14 (0.15), residues: 1291 sheet: -0.59 (0.28), residues: 321 loop : -2.07 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 321 HIS 0.004 0.001 HIS D 430 PHE 0.031 0.001 PHE C 514 TYR 0.016 0.001 TYR D1282 ARG 0.008 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 251 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.9411 (tp) cc_final: 0.9012 (tp) REVERT: B 18 GLN cc_start: 0.9514 (pm20) cc_final: 0.9297 (pm20) REVERT: B 125 LYS cc_start: 0.8743 (pttp) cc_final: 0.8306 (pptt) REVERT: C 165 HIS cc_start: 0.9133 (t-90) cc_final: 0.8650 (t70) REVERT: C 316 GLU cc_start: 0.9006 (mp0) cc_final: 0.8614 (tp30) REVERT: C 369 MET cc_start: 0.8989 (tpt) cc_final: 0.8723 (tpt) REVERT: C 471 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 548 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8546 (mtt180) REVERT: C 603 ILE cc_start: 0.9698 (pt) cc_final: 0.9404 (mt) REVERT: C 966 ILE cc_start: 0.7774 (mt) cc_final: 0.7402 (tp) REVERT: D 15 GLU cc_start: 0.9068 (pt0) cc_final: 0.8626 (tm-30) REVERT: D 113 HIS cc_start: 0.8989 (t-170) cc_final: 0.8331 (t70) REVERT: D 117 LEU cc_start: 0.8598 (tt) cc_final: 0.8319 (tp) REVERT: D 130 MET cc_start: 0.9540 (mtt) cc_final: 0.9201 (ttm) REVERT: D 189 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9343 (tt) REVERT: D 339 ARG cc_start: 0.9243 (tpp-160) cc_final: 0.8825 (mtt180) REVERT: D 706 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8213 (t) REVERT: D 807 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8906 (mt) REVERT: D 826 ILE cc_start: 0.9320 (pt) cc_final: 0.8914 (mt) REVERT: D 1040 MET cc_start: 0.8726 (mtt) cc_final: 0.8358 (mmt) REVERT: D 1159 ILE cc_start: 0.5153 (OUTLIER) cc_final: 0.4953 (mm) REVERT: E 41 GLU cc_start: 0.9246 (tt0) cc_final: 0.9030 (tm-30) REVERT: E 67 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9106 (mmm160) REVERT: M 181 ARG cc_start: 0.9186 (mtp180) cc_final: 0.8764 (mmm160) REVERT: M 376 MET cc_start: 0.5726 (mmm) cc_final: 0.4639 (mmp) outliers start: 74 outliers final: 60 residues processed: 310 average time/residue: 0.3651 time to fit residues: 186.3724 Evaluate side-chains 309 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1306 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.123485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077236 restraints weight = 68168.311| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.14 r_work: 0.2837 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28892 Z= 0.295 Angle : 0.725 15.069 39691 Z= 0.367 Chirality : 0.044 0.308 4774 Planarity : 0.004 0.084 4889 Dihedral : 17.422 178.583 4887 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.48 % Favored : 89.54 % Rotamer: Outliers : 2.90 % Allowed : 20.22 % Favored : 76.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3567 helix: 1.15 (0.15), residues: 1291 sheet: -0.58 (0.28), residues: 324 loop : -2.07 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 321 HIS 0.004 0.001 HIS D 80 PHE 0.024 0.002 PHE C 80 TYR 0.013 0.001 TYR D 631 ARG 0.013 0.001 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6402.34 seconds wall clock time: 115 minutes 29.73 seconds (6929.73 seconds total)