Starting phenix.real_space_refine on Sat Aug 10 05:06:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/08_2024/8rea_19080.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/08_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_19080/08_2024/8rea_19080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/08_2024/8rea_19080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/08_2024/8rea_19080.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rea_19080/08_2024/8rea_19080.cif" } 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-5409/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: 15.10, 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: 12.08 Conformation dependent library (CDL) restraints added in 5.4 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: 9.92 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: 14.39 Time building geometry restraints manager: 12.83 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 3.040 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.183 3.040 nonbonded pdb=" O LEU D1356 " pdb=" NE2 HIS D1366 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR D 262 " pdb=" OD1 ASP D 267 " model vdw 2.220 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 1.190 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 89.560 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.990 ------------------------------------------------------------------------------- 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 : 3.158 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: 0.4452 time to fit residues: 161.3280 Evaluate side-chains 157 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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: 8.9990 chunk 283 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 151 optimal weight: 40.0000 chunk 293 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- 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 128 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1236 ASN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN D1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 29442 Z= 0.558 Angle : 0.746 11.025 40444 Z= 0.394 Chirality : 0.047 0.210 4813 Planarity : 0.006 0.114 4961 Dihedral : 15.987 176.753 5071 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 5.51 % Allowed : 23.74 % Favored : 70.75 % 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: -0.60 (0.14), residues: 3644 helix: 1.01 (0.14), residues: 1345 sheet: -0.02 (0.27), residues: 393 loop : -1.58 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 115 HIS 0.008 0.002 HIS C1237 PHE 0.019 0.002 PHE D 7 TYR 0.025 0.002 TYR M 461 ARG 0.007 0.001 ARG D 220 *********************** 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 300 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 156 time to evaluate : 3.197 Fit side-chains revert: symmetry clash REVERT: C 796 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8627 (pp) REVERT: C 972 PHE cc_start: 0.4172 (OUTLIER) cc_final: 0.3655 (m-10) REVERT: D 9 LYS cc_start: 0.6568 (pttm) cc_final: 0.6067 (ptpt) REVERT: D 706 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8554 (m) REVERT: D 883 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7155 (ptm160) REVERT: D 1028 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5650 (mm) REVERT: D 1040 MET cc_start: 0.1539 (tpt) cc_final: 0.0742 (mmm) REVERT: M 206 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: M 280 LYS cc_start: 0.7203 (mmmm) cc_final: 0.6559 (pttt) REVERT: M 365 MET cc_start: 0.7523 (ppp) cc_final: 0.7090 (ptp) REVERT: M 460 LYS cc_start: 0.7792 (tttt) cc_final: 0.7331 (mmtt) outliers start: 144 outliers final: 74 residues processed: 285 average time/residue: 0.3706 time to fit residues: 174.8253 Evaluate side-chains 222 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 142 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR 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 204 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain B residue 59 VAL 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 B residue 146 VAL Chi-restraints excluded: chain B residue 223 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 144 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 209 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 420 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 940 GLU 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 1096 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 706 VAL 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 1028 ILE 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 E residue 10 VAL Chi-restraints excluded: chain E residue 54 ILE 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: 8.9990 chunk 105 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 367 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** D 294 ASN D 488 ASN M 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29442 Z= 0.277 Angle : 0.591 11.145 40444 Z= 0.310 Chirality : 0.042 0.183 4813 Planarity : 0.005 0.088 4961 Dihedral : 15.906 176.582 5069 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 4.44 % Allowed : 24.92 % Favored : 70.64 % 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: -0.31 (0.14), residues: 3644 helix: 1.37 (0.15), residues: 1336 sheet: 0.12 (0.27), residues: 397 loop : -1.50 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.003 0.001 HIS D 364 PHE 0.013 0.001 PHE C 405 TYR 0.017 0.001 TYR M 112 ARG 0.007 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 267 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 151 time to evaluate : 3.273 Fit side-chains revert: symmetry clash REVERT: C 359 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5408 (tmt90) REVERT: C 972 PHE cc_start: 0.3952 (OUTLIER) cc_final: 0.3625 (m-10) REVERT: D 883 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7107 (ptm160) REVERT: D 1040 MET cc_start: 0.1038 (tpt) cc_final: 0.0342 (mmm) REVERT: M 206 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: M 217 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7078 (ttm110) REVERT: M 279 ARG cc_start: 0.6374 (ptm-80) cc_final: 0.5998 (ptm-80) REVERT: M 280 LYS cc_start: 0.7063 (mmmm) cc_final: 0.6844 (pttt) REVERT: M 365 MET cc_start: 0.7531 (ppp) cc_final: 0.7084 (ptp) outliers start: 116 outliers final: 57 residues processed: 252 average time/residue: 0.4002 time to fit residues: 166.5373 Evaluate side-chains 203 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 142 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE 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 A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE 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 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 359 ARG Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 717 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 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 117 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 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 722 ILE Chi-restraints excluded: chain D residue 801 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 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU 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 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: 4.9990 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 361 optimal weight: 50.0000 chunk 178 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2319 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= 0.260 Angle : 0.580 11.550 40444 Z= 0.302 Chirality : 0.042 0.259 4813 Planarity : 0.004 0.070 4961 Dihedral : 15.843 176.918 5069 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.41 % Rotamer: Outliers : 4.56 % Allowed : 24.50 % Favored : 70.94 % 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: -0.19 (0.14), residues: 3644 helix: 1.55 (0.15), residues: 1331 sheet: 0.15 (0.27), residues: 396 loop : -1.47 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS D1366 PHE 0.011 0.001 PHE C 405 TYR 0.021 0.001 TYR M 461 ARG 0.006 0.000 ARG C 378 *********************** 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 270 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 151 time to evaluate : 3.202 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.7400 (m-10) cc_final: 0.7186 (m-10) REVERT: C 1265 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8236 (t80) REVERT: D 883 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7054 (ptm160) REVERT: D 1040 MET cc_start: 0.1027 (tpt) cc_final: 0.0641 (mmm) REVERT: M 206 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6873 (m-10) REVERT: M 279 ARG cc_start: 0.6202 (ptm-80) cc_final: 0.5837 (ptm-80) REVERT: M 365 MET cc_start: 0.7594 (ppp) cc_final: 0.7200 (ptp) outliers start: 119 outliers final: 76 residues processed: 259 average time/residue: 0.3789 time to fit residues: 162.1041 Evaluate side-chains 224 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 145 time to evaluate : 3.505 ------------------------------------------------------------------------------- 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 160 HIS 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 A residue 280 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 32 GLU 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 129 VAL Chi-restraints excluded: chain B residue 132 HIS 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 144 VAL 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 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 717 VAL 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 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR 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 568 SER Chi-restraints excluded: chain D residue 682 VAL 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 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 932 MET 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 E residue 58 LEU Chi-restraints excluded: chain M residue 158 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 40.0000 chunk 205 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 0.6980 chunk 324 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29442 Z= 0.201 Angle : 0.548 12.728 40444 Z= 0.285 Chirality : 0.041 0.177 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.730 176.510 5069 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 4.06 % Allowed : 24.92 % Favored : 71.02 % 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: -0.06 (0.14), residues: 3644 helix: 1.72 (0.15), residues: 1340 sheet: 0.22 (0.26), residues: 406 loop : -1.47 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.002 0.001 HIS D1366 PHE 0.011 0.001 PHE C 405 TYR 0.011 0.001 TYR M 112 ARG 0.004 0.000 ARG D 47 *********************** 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 : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1265 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8228 (t80) REVERT: D 883 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7045 (ptm160) REVERT: D 1040 MET cc_start: 0.1107 (tpt) cc_final: 0.0705 (mmm) REVERT: M 115 GLU cc_start: 0.7520 (tp30) cc_final: 0.7283 (tp30) REVERT: M 206 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: M 217 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7101 (ttm110) REVERT: M 279 ARG cc_start: 0.6156 (ptm-80) cc_final: 0.5940 (ptm-80) REVERT: M 280 LYS cc_start: 0.7010 (mmmm) cc_final: 0.6742 (pttt) REVERT: M 365 MET cc_start: 0.7581 (ppp) cc_final: 0.7193 (ptp) REVERT: M 460 LYS cc_start: 0.8356 (tppt) cc_final: 0.7585 (mmmt) outliers start: 106 outliers final: 68 residues processed: 248 average time/residue: 0.3807 time to fit residues: 158.0804 Evaluate side-chains 213 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 142 time to evaluate : 3.461 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 92 VAL 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 198 LEU 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 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 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 871 VAL 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 1159 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 95 THR 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 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 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 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU 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 M residue 111 VAL Chi-restraints excluded: chain M residue 206 PHE 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: 10.0000 chunk 325 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 361 optimal weight: 40.0000 chunk 300 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29442 Z= 0.324 Angle : 0.609 16.560 40444 Z= 0.314 Chirality : 0.042 0.203 4813 Planarity : 0.004 0.066 4961 Dihedral : 15.800 176.126 5069 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 4.33 % Allowed : 24.92 % Favored : 70.75 % 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: 1.65 (0.15), residues: 1338 sheet: 0.22 (0.26), residues: 405 loop : -1.52 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 409 HIS 0.004 0.001 HIS D 777 PHE 0.010 0.001 PHE D 7 TYR 0.013 0.001 TYR M 112 ARG 0.005 0.000 ARG M 184 *********************** 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 258 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 145 time to evaluate : 3.237 Fit side-chains revert: symmetry clash REVERT: C 1265 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8268 (t80) REVERT: D 883 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7122 (ptm160) REVERT: D 1040 MET cc_start: 0.1390 (tpt) cc_final: 0.1150 (mmm) REVERT: M 206 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: M 279 ARG cc_start: 0.6313 (ptm-80) cc_final: 0.5907 (ptm-80) REVERT: M 365 MET cc_start: 0.7591 (ppp) cc_final: 0.7195 (ptp) outliers start: 113 outliers final: 79 residues processed: 246 average time/residue: 0.3674 time to fit residues: 152.2491 Evaluate side-chains 220 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 138 time to evaluate : 3.390 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 92 VAL 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 198 LEU Chi-restraints excluded: chain B residue 206 GLU 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 144 VAL 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 289 VAL 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 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE 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 95 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 240 THR 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 568 SER Chi-restraints excluded: chain D residue 682 VAL 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 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS 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 158 ILE Chi-restraints excluded: chain M residue 172 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 264 optimal weight: 4.9990 chunk 204 optimal weight: 50.0000 chunk 304 optimal weight: 2.9990 chunk 202 optimal weight: 50.0000 chunk 360 optimal weight: 50.0000 chunk 225 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29442 Z= 0.317 Angle : 0.597 14.992 40444 Z= 0.310 Chirality : 0.042 0.194 4813 Planarity : 0.004 0.064 4961 Dihedral : 15.834 176.044 5069 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 4.44 % Allowed : 24.92 % Favored : 70.64 % 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: -0.17 (0.14), residues: 3644 helix: 1.63 (0.15), residues: 1340 sheet: 0.15 (0.26), residues: 403 loop : -1.54 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.004 0.001 HIS D 777 PHE 0.010 0.001 PHE D 7 TYR 0.013 0.001 TYR M 112 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 257 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 141 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1265 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8279 (t80) REVERT: D 883 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7062 (ptm160) REVERT: D 1040 MET cc_start: 0.1734 (tpt) cc_final: 0.1328 (mmm) REVERT: M 206 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: M 279 ARG cc_start: 0.6204 (ptm-80) cc_final: 0.5543 (ptm-80) REVERT: M 280 LYS cc_start: 0.7160 (mmmm) cc_final: 0.6790 (pttt) REVERT: M 365 MET cc_start: 0.7622 (ppp) cc_final: 0.7166 (ptp) REVERT: M 460 LYS cc_start: 0.8334 (tppt) cc_final: 0.7532 (mmmt) outliers start: 116 outliers final: 90 residues processed: 243 average time/residue: 0.3736 time to fit residues: 152.5435 Evaluate side-chains 228 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 135 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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 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 A residue 282 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER 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 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 198 LEU 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 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL 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 442 VAL 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 513 GLN 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 650 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 975 ILE 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 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 21 LYS 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 95 THR Chi-restraints excluded: chain D residue 111 THR 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 370 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 VAL 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 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS 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 111 VAL 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 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3204 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= 0.238 Angle : 0.575 14.871 40444 Z= 0.296 Chirality : 0.042 0.230 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.768 176.008 5069 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.50 % Rotamer: Outliers : 3.79 % Allowed : 25.54 % Favored : 70.67 % 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: 1.74 (0.15), residues: 1344 sheet: 0.22 (0.27), residues: 403 loop : -1.53 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 115 HIS 0.003 0.001 HIS D 777 PHE 0.010 0.001 PHE C 405 TYR 0.013 0.001 TYR M 112 ARG 0.005 0.000 ARG D 47 *********************** 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 238 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 139 time to evaluate : 3.276 Fit side-chains revert: symmetry clash REVERT: A 268 ASN cc_start: 0.9029 (m110) cc_final: 0.8714 (m110) REVERT: C 1265 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8254 (t80) REVERT: C 1315 MET cc_start: 0.6901 (tpp) cc_final: 0.6700 (ttp) REVERT: D 9 LYS cc_start: 0.6843 (pttm) cc_final: 0.6462 (pttp) REVERT: D 883 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7101 (ptm160) REVERT: D 1040 MET cc_start: 0.1764 (tpt) cc_final: 0.1384 (mmm) REVERT: M 206 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6744 (m-10) REVERT: M 279 ARG cc_start: 0.6083 (ptm-80) cc_final: 0.5494 (ptm-80) REVERT: M 280 LYS cc_start: 0.7149 (mmmm) cc_final: 0.6765 (pttt) REVERT: M 365 MET cc_start: 0.7572 (ppp) cc_final: 0.7094 (ptp) REVERT: M 460 LYS cc_start: 0.8343 (tppt) cc_final: 0.7589 (mmmt) outliers start: 99 outliers final: 83 residues processed: 227 average time/residue: 0.3778 time to fit residues: 146.1382 Evaluate side-chains 225 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 139 time to evaluate : 3.124 ------------------------------------------------------------------------------- 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 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 A residue 282 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 6 THR 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 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 GLU 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 144 VAL 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 289 VAL 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 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL 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 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1046 VAL 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 1265 PHE 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 71 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 111 THR 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 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 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 VAL 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 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS 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 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 30.0000 chunk 345 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 335 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 303 optimal weight: 30.0000 chunk 317 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29442 Z= 0.224 Angle : 0.567 14.522 40444 Z= 0.292 Chirality : 0.041 0.234 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.706 175.827 5069 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 3.91 % Allowed : 25.42 % Favored : 70.67 % 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: -0.03 (0.14), residues: 3644 helix: 1.80 (0.15), residues: 1343 sheet: 0.20 (0.26), residues: 411 loop : -1.51 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.006 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 244 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 142 time to evaluate : 3.333 Fit side-chains revert: symmetry clash REVERT: A 268 ASN cc_start: 0.9029 (m-40) cc_final: 0.8654 (m110) REVERT: C 1265 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8241 (t80) REVERT: D 883 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7058 (ptm160) REVERT: D 1040 MET cc_start: 0.1703 (tpt) cc_final: 0.1406 (mmm) REVERT: M 206 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: M 217 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7261 (ttm110) REVERT: M 279 ARG cc_start: 0.5974 (ptm-80) cc_final: 0.5495 (ptm-80) REVERT: M 280 LYS cc_start: 0.7076 (mmmm) cc_final: 0.6725 (pttt) REVERT: M 360 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5485 (pt0) REVERT: M 365 MET cc_start: 0.7595 (ppp) cc_final: 0.7143 (ptp) outliers start: 102 outliers final: 83 residues processed: 232 average time/residue: 0.3748 time to fit residues: 145.3633 Evaluate side-chains 224 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 137 time to evaluate : 3.021 ------------------------------------------------------------------------------- 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 130 ILE Chi-restraints excluded: chain A residue 160 HIS 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 A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 6 THR 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 132 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 GLU 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 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL 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 400 VAL 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 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 975 ILE 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 1265 PHE 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 95 THR Chi-restraints excluded: chain D residue 111 THR 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 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 484 MET Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 786 THR 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 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS 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 333 LEU Chi-restraints excluded: chain M residue 360 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 3.9990 chunk 355 optimal weight: 0.9980 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: 30.0000 chunk 296 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29442 Z= 0.318 Angle : 0.615 14.379 40444 Z= 0.317 Chirality : 0.042 0.227 4813 Planarity : 0.004 0.066 4961 Dihedral : 15.812 175.648 5067 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.81 % Rotamer: Outliers : 3.60 % Allowed : 25.92 % Favored : 70.48 % 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: -0.09 (0.14), residues: 3644 helix: 1.73 (0.15), residues: 1343 sheet: 0.19 (0.27), residues: 400 loop : -1.52 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 115 HIS 0.008 0.001 HIS A 117 PHE 0.012 0.001 PHE D 7 TYR 0.013 0.001 TYR M 112 ARG 0.011 0.000 ARG C 478 ********************** 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 228 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 134 time to evaluate : 3.366 Fit side-chains revert: symmetry clash REVERT: A 117 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7749 (t-90) REVERT: A 268 ASN cc_start: 0.9121 (m-40) cc_final: 0.8784 (m110) REVERT: C 1265 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8295 (t80) REVERT: D 9 LYS cc_start: 0.6785 (pttm) cc_final: 0.6278 (pttp) REVERT: D 883 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: D 1040 MET cc_start: 0.1542 (tpt) cc_final: 0.1302 (mmm) REVERT: M 206 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6863 (m-10) REVERT: M 279 ARG cc_start: 0.6115 (ptm-80) cc_final: 0.5549 (ptm-80) REVERT: M 365 MET cc_start: 0.7586 (ppp) cc_final: 0.7124 (ptp) outliers start: 94 outliers final: 77 residues processed: 219 average time/residue: 0.3750 time to fit residues: 139.0483 Evaluate side-chains 214 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 133 time to evaluate : 3.271 ------------------------------------------------------------------------------- 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 117 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 6 THR 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 132 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 206 GLU 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 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL 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 400 VAL 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 487 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 975 ILE 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 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE 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 95 THR Chi-restraints excluded: chain D residue 111 THR 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 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 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 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS 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 287 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 235 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 90 optimal weight: 0.0170 chunk 273 optimal weight: 2.9990 chunk 43 optimal weight: 40.0000 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048757 restraints weight = 113515.098| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.34 r_work: 0.2763 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29442 Z= 0.207 Angle : 0.578 14.291 40444 Z= 0.296 Chirality : 0.041 0.226 4813 Planarity : 0.004 0.062 4961 Dihedral : 15.767 175.364 5067 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 3.14 % Allowed : 26.45 % Favored : 70.41 % 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: -0.04 (0.14), residues: 3644 helix: 1.79 (0.15), residues: 1345 sheet: 0.22 (0.26), residues: 411 loop : -1.51 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 115 HIS 0.004 0.001 HIS A 117 PHE 0.009 0.001 PHE C 405 TYR 0.012 0.001 TYR M 112 ARG 0.007 0.000 ARG C 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5400.76 seconds wall clock time: 98 minutes 44.33 seconds (5924.33 seconds total)