Starting phenix.real_space_refine on Thu Mar 21 00:13:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/03_2024/8rea_19080.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/03_2024/8rea_19080.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/8rea_19080/03_2024/8rea_19080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/03_2024/8rea_19080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/03_2024/8rea_19080.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/03_2024/8rea_19080.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 100 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 17773 2.51 5 N 5123 2.21 5 O 5724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C ASP 648": "OD1" <-> "OD2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "C PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1143": "OE1" <-> "OE2" Residue "C PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1188": "OD1" <-> "OD2" Residue "C GLU 1219": "OE1" <-> "OE2" Residue "C TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 652": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 827": "OE1" <-> "OE2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D ASP 1021": "OD1" <-> "OD2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D ASP 1305": "OD1" <-> "OD2" Residue "D GLU 1343": "OE1" <-> "OE2" Residue "D GLU 1349": "OE1" <-> "OE2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "M TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9682 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2354 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 16, 'TRANS': 363} Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 3, 'GLU:plan': 25, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 395 Chain: "N" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 899 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "T" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1051 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14703 SG CYS D 70 105.384 115.698 91.370 1.00 25.43 S ATOM 14832 SG CYS D 88 103.734 115.861 95.297 1.00 28.14 S ATOM 20325 SG CYS D 814 101.741 47.710 89.204 1.00 22.49 S ATOM 20945 SG CYS D 898 98.843 47.324 88.719 1.00 14.48 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.98 Time building chain proxies: 15.05, per 1000 atoms: 0.52 Number of scatterers: 28821 At special positions: 0 Unit cell: (144.1, 172.7, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 100 15.00 Mg 1 11.99 O 5724 8.00 N 5123 7.00 C 17773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 44 sheets defined 39.6% alpha, 13.6% beta 38 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.848A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.849A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.934A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.696A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.585A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.914A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.521A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.737A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.703A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.825A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.880A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.564A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.693A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.564A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.629A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.571A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 removed outlier: 3.811A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.520A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.230A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.735A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.772A 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 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.988A 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 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.806A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.696A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.771A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.655A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.374A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.640A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.503A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.808A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.719A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.524A pdb=" N THR D 14 " --> pdb=" O GLN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.040A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.850A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.537A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.631A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.191A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.807A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.641A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (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 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.758A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.731A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.045A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.889A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.518A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.882A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.636A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.749A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.937A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.740A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.798A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 removed outlier: 3.590A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.611A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.892A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 129 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.769A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.561A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 Processing helix chain 'M' and resid 212 through 218 removed outlier: 3.600A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.574A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.840A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 351 removed outlier: 3.886A pdb=" N ALA M 326 " --> pdb=" O ASN M 322 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M 327 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 removed outlier: 3.983A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.617A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.535A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.602A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 6.658A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.408A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.679A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.323A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.537A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 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: 5.860A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.816A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.816A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.043A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.507A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.154A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.563A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.745A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.403A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.539A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.539A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.609A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.871A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 112 removed outlier: 8.477A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.902A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.046A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.822A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 5.080A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.764A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE8, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.361A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1140 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 14.55 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9540 1.34 - 1.46: 5442 1.46 - 1.58: 14094 1.58 - 1.70: 196 1.70 - 1.82: 170 Bond restraints: 29442 Sorted by residual: bond pdb=" C3' DA N -2 " pdb=" O3' DA N -2 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.331 1.367 -0.036 2.83e-02 1.25e+03 1.59e+00 bond pdb=" CB ASN D 45 " pdb=" CG ASN D 45 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CB PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.42e+00 bond pdb=" CA ILE D 646 " pdb=" CB ILE D 646 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.41e+00 ... (remaining 29437 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.92: 1084 105.92 - 112.95: 16251 112.95 - 119.98: 9743 119.98 - 127.00: 12926 127.00 - 134.03: 440 Bond angle restraints: 40444 Sorted by residual: angle pdb=" CB MET C 800 " pdb=" CG MET C 800 " pdb=" SD MET C 800 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N GLU M 325 " pdb=" CA GLU M 325 " pdb=" C GLU M 325 " ideal model delta sigma weight residual 113.18 108.29 4.89 1.33e+00 5.65e-01 1.35e+01 angle pdb=" CA PRO C 567 " pdb=" N PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 112.00 107.24 4.76 1.40e+00 5.10e-01 1.16e+01 angle pdb=" N GLY D 613 " pdb=" CA GLY D 613 " pdb=" C GLY D 613 " ideal model delta sigma weight residual 110.29 114.47 -4.18 1.28e+00 6.10e-01 1.07e+01 angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 113.53 110.34 3.19 9.80e-01 1.04e+00 1.06e+01 ... (remaining 40439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 16774 35.50 - 71.00: 872 71.00 - 106.49: 37 106.49 - 141.99: 2 141.99 - 177.49: 1 Dihedral angle restraints: 17686 sinusoidal: 7140 harmonic: 10546 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 140.76 39.24 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" C4' DG N 4 " pdb=" C3' DG N 4 " pdb=" O3' DG N 4 " pdb=" P DA N 5 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE D 338 " pdb=" C PHE D 338 " pdb=" N ARG D 339 " pdb=" CA ARG D 339 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 17683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3909 0.050 - 0.099: 720 0.099 - 0.149: 178 0.149 - 0.199: 5 0.199 - 0.249: 1 Chirality restraints: 4813 Sorted by residual: chirality pdb=" CB ILE M 170 " pdb=" CA ILE M 170 " pdb=" CG1 ILE M 170 " pdb=" CG2 ILE M 170 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB THR M 386 " pdb=" CA THR M 386 " pdb=" OG1 THR M 386 " pdb=" CG2 THR M 386 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CG LEU C 210 " pdb=" CB LEU C 210 " pdb=" CD1 LEU C 210 " pdb=" CD2 LEU C 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 4810 not shown) Planarity restraints: 4961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.102 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO C 567 " -0.266 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 273 " -0.065 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO M 274 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 274 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 274 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO D1139 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.040 5.00e-02 4.00e+02 ... (remaining 4958 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 459 2.67 - 3.22: 26848 3.22 - 3.78: 43599 3.78 - 4.34: 57204 4.34 - 4.90: 95113 Nonbonded interactions: 223223 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.108 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb=" O2' C R 3 " model vdw 2.173 2.440 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.183 2.440 nonbonded pdb=" O LEU D1356 " pdb=" NE2 HIS D1366 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR D 262 " pdb=" OD1 ASP D 267 " model vdw 2.220 2.440 ... (remaining 223218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.570 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 86.440 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29442 Z= 0.171 Angle : 0.604 12.733 40444 Z= 0.326 Chirality : 0.041 0.249 4813 Planarity : 0.005 0.154 4961 Dihedral : 18.952 177.491 10882 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.23 % Allowed : 27.79 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3644 helix: 1.10 (0.15), residues: 1312 sheet: 0.10 (0.27), residues: 386 loop : -1.43 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.011 0.001 HIS B 128 PHE 0.021 0.001 PHE M 354 TYR 0.016 0.001 TYR M 112 ARG 0.013 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 3.380 Fit side-chains revert: symmetry clash REVERT: D 1040 MET cc_start: 0.0469 (tpt) cc_final: -0.0453 (mmp) REVERT: M 280 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6461 (pttt) REVERT: M 365 MET cc_start: 0.7370 (ppp) cc_final: 0.6985 (ptp) REVERT: M 460 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7305 (mmtt) outliers start: 6 outliers final: 3 residues processed: 228 average time/residue: 0.4135 time to fit residues: 152.1687 Evaluate side-chains 157 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain D residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 151 optimal weight: 50.0000 chunk 293 optimal weight: 0.0870 chunk 113 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 overall best weight: 6.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN D1268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29442 Z= 0.348 Angle : 0.617 10.426 40444 Z= 0.325 Chirality : 0.043 0.213 4813 Planarity : 0.005 0.109 4961 Dihedral : 15.811 177.714 5071 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.37 % Favored : 93.61 % Rotamer: Outliers : 4.71 % Allowed : 24.69 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3644 helix: 1.29 (0.15), residues: 1342 sheet: 0.06 (0.27), residues: 387 loop : -1.46 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 115 HIS 0.005 0.001 HIS B 128 PHE 0.013 0.001 PHE M 354 TYR 0.025 0.001 TYR M 461 ARG 0.008 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 159 time to evaluate : 3.053 Fit side-chains revert: symmetry clash REVERT: C 972 PHE cc_start: 0.3971 (OUTLIER) cc_final: 0.3448 (m-10) REVERT: D 9 LYS cc_start: 0.6472 (pttm) cc_final: 0.6032 (ptpt) REVERT: D 883 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: D 1040 MET cc_start: 0.1329 (tpt) cc_final: 0.0335 (mmm) REVERT: M 206 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: M 279 ARG cc_start: 0.6442 (ptm-80) cc_final: 0.6217 (ptm-80) REVERT: M 280 LYS cc_start: 0.7013 (mmmm) cc_final: 0.6726 (pttt) REVERT: M 460 LYS cc_start: 0.7777 (tttt) cc_final: 0.7298 (mmtt) outliers start: 123 outliers final: 58 residues processed: 269 average time/residue: 0.3849 time to fit residues: 175.4542 Evaluate side-chains 210 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 149 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 282 optimal weight: 0.0770 chunk 231 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 340 optimal weight: 40.0000 chunk 367 optimal weight: 30.0000 chunk 303 optimal weight: 30.0000 chunk 337 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 128 HIS C 659 GLN C 856 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 716 GLN D1249 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29442 Z= 0.190 Angle : 0.538 9.637 40444 Z= 0.282 Chirality : 0.041 0.181 4813 Planarity : 0.004 0.081 4961 Dihedral : 15.708 177.456 5069 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 3.79 % Allowed : 26.15 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3644 helix: 1.59 (0.15), residues: 1339 sheet: 0.13 (0.26), residues: 418 loop : -1.47 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.008 0.001 HIS B 128 PHE 0.011 0.001 PHE C 405 TYR 0.014 0.001 TYR M 112 ARG 0.006 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 158 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8427 (tp) cc_final: 0.8200 (tp) REVERT: C 972 PHE cc_start: 0.3988 (OUTLIER) cc_final: 0.3698 (m-10) REVERT: D 9 LYS cc_start: 0.6426 (pttm) cc_final: 0.5950 (ptpt) REVERT: D 883 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6970 (ptm160) REVERT: D 1040 MET cc_start: 0.1199 (tpt) cc_final: 0.0515 (mmm) REVERT: M 206 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: M 279 ARG cc_start: 0.6234 (ptm-80) cc_final: 0.6032 (ptm-80) REVERT: M 365 MET cc_start: 0.7768 (ptt) cc_final: 0.7487 (ptp) outliers start: 99 outliers final: 42 residues processed: 241 average time/residue: 0.3673 time to fit residues: 147.3202 Evaluate side-chains 196 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 361 optimal weight: 50.0000 chunk 178 optimal weight: 4.9990 chunk 323 optimal weight: 0.0050 chunk 97 optimal weight: 7.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 518 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 424 ASN D 488 ASN M 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29442 Z= 0.154 Angle : 0.528 11.394 40444 Z= 0.271 Chirality : 0.040 0.222 4813 Planarity : 0.004 0.066 4961 Dihedral : 15.607 177.783 5069 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.05 % Rotamer: Outliers : 3.45 % Allowed : 26.23 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3644 helix: 1.72 (0.15), residues: 1346 sheet: 0.24 (0.26), residues: 408 loop : -1.43 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 33 HIS 0.010 0.001 HIS B 128 PHE 0.010 0.001 PHE M 402 TYR 0.011 0.001 TYR M 112 ARG 0.012 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 163 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.8416 (tp) cc_final: 0.8196 (tp) REVERT: D 9 LYS cc_start: 0.6531 (pttm) cc_final: 0.6014 (ptpt) REVERT: D 883 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6969 (ptm160) REVERT: D 1040 MET cc_start: 0.1275 (tpt) cc_final: 0.0475 (mmm) REVERT: M 206 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: M 460 LYS cc_start: 0.8312 (tppt) cc_final: 0.7555 (mmmt) REVERT: M 461 TYR cc_start: 0.7506 (m-80) cc_final: 0.7285 (m-80) outliers start: 90 outliers final: 50 residues processed: 240 average time/residue: 0.3814 time to fit residues: 153.9808 Evaluate side-chains 208 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 20.0000 chunk 205 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 308 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS C 214 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29442 Z= 0.273 Angle : 0.567 12.333 40444 Z= 0.293 Chirality : 0.041 0.210 4813 Planarity : 0.004 0.069 4961 Dihedral : 15.656 176.982 5069 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 4.06 % Allowed : 25.92 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3644 helix: 1.77 (0.15), residues: 1344 sheet: 0.21 (0.26), residues: 406 loop : -1.44 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.005 0.001 HIS B 128 PHE 0.011 0.001 PHE M 402 TYR 0.013 0.001 TYR D 537 ARG 0.018 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 154 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 883 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7038 (ptm160) REVERT: D 1040 MET cc_start: 0.0787 (tpt) cc_final: 0.0477 (mmm) REVERT: M 206 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: M 279 ARG cc_start: 0.5004 (ptm-80) cc_final: 0.4647 (ptm-80) REVERT: M 365 MET cc_start: 0.7753 (ptt) cc_final: 0.7479 (ptp) outliers start: 106 outliers final: 74 residues processed: 242 average time/residue: 0.3870 time to fit residues: 157.8948 Evaluate side-chains 222 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 146 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 361 optimal weight: 40.0000 chunk 300 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 119 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29442 Z= 0.256 Angle : 0.557 12.527 40444 Z= 0.287 Chirality : 0.041 0.180 4813 Planarity : 0.004 0.060 4961 Dihedral : 15.663 177.104 5069 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 4.13 % Allowed : 26.07 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3644 helix: 1.80 (0.15), residues: 1339 sheet: 0.24 (0.26), residues: 415 loop : -1.44 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS B 128 PHE 0.011 0.001 PHE C 972 TYR 0.011 0.001 TYR M 112 ARG 0.004 0.000 ARG M 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 148 time to evaluate : 3.148 Fit side-chains revert: symmetry clash REVERT: C 1018 TYR cc_start: 0.5333 (m-80) cc_final: 0.5118 (m-80) REVERT: D 883 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7053 (ptm160) REVERT: D 1040 MET cc_start: 0.1131 (tpt) cc_final: 0.0738 (mmm) REVERT: E 69 ARG cc_start: 0.7741 (ptm-80) cc_final: 0.7513 (ptm-80) REVERT: M 206 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: M 279 ARG cc_start: 0.5230 (ptm-80) cc_final: 0.4933 (ptm-80) REVERT: M 365 MET cc_start: 0.7753 (ptt) cc_final: 0.7451 (ptp) REVERT: M 460 LYS cc_start: 0.8155 (tppt) cc_final: 0.7383 (mmmt) outliers start: 108 outliers final: 79 residues processed: 241 average time/residue: 0.3524 time to fit residues: 145.9291 Evaluate side-chains 223 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 142 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 50.0000 chunk 40 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 264 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 202 optimal weight: 40.0000 chunk 360 optimal weight: 50.0000 chunk 225 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29442 Z= 0.357 Angle : 0.622 13.451 40444 Z= 0.321 Chirality : 0.043 0.324 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.820 176.671 5069 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.81 % Rotamer: Outliers : 4.67 % Allowed : 25.34 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3644 helix: 1.67 (0.15), residues: 1346 sheet: 0.23 (0.27), residues: 397 loop : -1.54 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 115 HIS 0.005 0.001 HIS B 128 PHE 0.011 0.001 PHE D 7 TYR 0.023 0.002 TYR D 140 ARG 0.005 0.000 ARG M 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 144 time to evaluate : 3.162 Fit side-chains revert: symmetry clash REVERT: C 1018 TYR cc_start: 0.5621 (m-80) cc_final: 0.5419 (m-80) REVERT: D 883 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7100 (ptm160) REVERT: D 1040 MET cc_start: 0.1485 (tpt) cc_final: 0.1230 (mmm) REVERT: M 206 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: M 365 MET cc_start: 0.7824 (ptt) cc_final: 0.7529 (ptp) outliers start: 122 outliers final: 86 residues processed: 252 average time/residue: 0.3726 time to fit residues: 158.9647 Evaluate side-chains 228 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 140 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 0.0570 chunk 143 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29442 Z= 0.219 Angle : 0.560 12.628 40444 Z= 0.288 Chirality : 0.041 0.191 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.741 176.790 5069 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.05 % Rotamer: Outliers : 3.71 % Allowed : 25.96 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3644 helix: 1.80 (0.15), residues: 1349 sheet: 0.30 (0.26), residues: 413 loop : -1.51 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.004 0.001 HIS B 128 PHE 0.011 0.001 PHE M 402 TYR 0.012 0.001 TYR M 112 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 144 time to evaluate : 3.223 Fit side-chains revert: symmetry clash REVERT: D 883 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7021 (ptm160) REVERT: M 206 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: M 460 LYS cc_start: 0.8297 (tppt) cc_final: 0.7574 (mmmt) outliers start: 97 outliers final: 85 residues processed: 231 average time/residue: 0.3565 time to fit residues: 141.0039 Evaluate side-chains 223 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 136 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 0.2980 chunk 345 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 202 optimal weight: 0.2980 chunk 146 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 303 optimal weight: 30.0000 chunk 317 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29442 Z= 0.243 Angle : 0.567 17.767 40444 Z= 0.291 Chirality : 0.041 0.188 4813 Planarity : 0.004 0.068 4961 Dihedral : 15.706 176.997 5069 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 3.83 % Allowed : 25.88 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3644 helix: 1.83 (0.15), residues: 1351 sheet: 0.27 (0.26), residues: 416 loop : -1.52 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.003 0.001 HIS D 777 PHE 0.009 0.001 PHE C 405 TYR 0.011 0.001 TYR M 112 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 137 time to evaluate : 3.301 Fit side-chains revert: symmetry clash REVERT: C 972 PHE cc_start: 0.4578 (OUTLIER) cc_final: 0.4291 (m-10) REVERT: D 883 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7051 (ptm160) REVERT: M 206 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6803 (m-10) REVERT: M 460 LYS cc_start: 0.8351 (tppt) cc_final: 0.7601 (mmmt) outliers start: 100 outliers final: 84 residues processed: 227 average time/residue: 0.3597 time to fit residues: 140.6301 Evaluate side-chains 222 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 135 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 372 optimal weight: 30.0000 chunk 342 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29442 Z= 0.299 Angle : 0.595 16.435 40444 Z= 0.306 Chirality : 0.042 0.186 4813 Planarity : 0.004 0.080 4961 Dihedral : 15.772 176.486 5069 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.11 % Rotamer: Outliers : 3.68 % Allowed : 26.07 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3644 helix: 1.73 (0.15), residues: 1353 sheet: 0.22 (0.26), residues: 413 loop : -1.55 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.004 0.001 HIS C1023 PHE 0.010 0.001 PHE D 7 TYR 0.012 0.001 TYR D 537 ARG 0.011 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 141 time to evaluate : 3.234 Fit side-chains revert: symmetry clash REVERT: D 9 LYS cc_start: 0.6770 (pttm) cc_final: 0.6341 (pttp) REVERT: D 883 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7110 (ptm160) REVERT: M 206 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: M 280 LYS cc_start: 0.7413 (pttt) cc_final: 0.7197 (ptpt) outliers start: 96 outliers final: 83 residues processed: 226 average time/residue: 0.3582 time to fit residues: 137.0462 Evaluate side-chains 222 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 137 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 333 LEU Chi-restraints excluded: chain M residue 365 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 43 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 297 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.072063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047844 restraints weight = 114836.410| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.32 r_work: 0.2733 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29442 Z= 0.340 Angle : 0.608 16.724 40444 Z= 0.314 Chirality : 0.042 0.192 4813 Planarity : 0.004 0.090 4961 Dihedral : 15.818 176.846 5067 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 3.48 % Allowed : 26.19 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3644 helix: 1.70 (0.15), residues: 1351 sheet: 0.10 (0.26), residues: 422 loop : -1.55 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 115 HIS 0.004 0.001 HIS D 777 PHE 0.009 0.001 PHE D 7 TYR 0.012 0.001 TYR M 112 ARG 0.006 0.000 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.45 seconds wall clock time: 92 minutes 56.27 seconds (5576.27 seconds total)