Starting phenix.real_space_refine on Sat Apr 6 03:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7n_18225/04_2024/8q7n_18225.pdb" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 206 5.16 5 C 33763 2.51 5 N 9963 2.21 5 O 11231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 GLU 409": "OE1" <-> "OE2" Residue "7 GLU 418": "OE1" <-> "OE2" Residue "7 GLU 427": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C GLU 573": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 799": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "K GLU 353": "OE1" <-> "OE2" Residue "K TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "X GLU 28": "OE1" <-> "OE2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X GLU 46": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "r GLU 76": "OE1" <-> "OE2" Residue "s GLU 3": "OE1" <-> "OE2" Residue "s GLU 61": "OE1" <-> "OE2" Residue "L GLU 153": "OE1" <-> "OE2" Residue "L GLU 182": "OE1" <-> "OE2" Residue "L GLU 370": "OE1" <-> "OE2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 409": "OE1" <-> "OE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 177": "OE1" <-> "OE2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N GLU 343": "OE1" <-> "OE2" Residue "N GLU 381": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A GLU 1235": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A PHE 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1376": "OE1" <-> "OE2" Residue "A GLU 1511": "OE1" <-> "OE2" Residue "A GLU 1587": "OE1" <-> "OE2" Residue "A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1770": "OE1" <-> "OE2" Residue "A GLU 1844": "OE1" <-> "OE2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A GLU 2006": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S GLU 260": "OE1" <-> "OE2" Residue "S GLU 268": "OE1" <-> "OE2" Residue "S GLU 284": "OE1" <-> "OE2" Residue "S GLU 286": "OE1" <-> "OE2" Residue "S GLU 305": "OE1" <-> "OE2" Residue "S GLU 340": "OE1" <-> "OE2" Residue "S GLU 352": "OE1" <-> "OE2" Residue "T GLU 860": "OE1" <-> "OE2" Residue "T GLU 871": "OE1" <-> "OE2" Residue "T GLU 873": "OE1" <-> "OE2" Residue "T GLU 897": "OE1" <-> "OE2" Residue "J GLU 455": "OE1" <-> "OE2" Residue "J GLU 462": "OE1" <-> "OE2" Residue "J GLU 488": "OE1" <-> "OE2" Residue "J GLU 512": "OE1" <-> "OE2" Residue "J GLU 513": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 55463 Number of models: 1 Model: "" Number of chains: 21 Chain: "5" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2420 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 39, 'rna3p_pyr': 57} Link IDs: {'rna2p': 18, 'rna3p': 96} Chain: "6" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1670 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 37, 'rna3p_pyr': 25} Link IDs: {'rna2p': 16, 'rna3p': 61} Chain: "7" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 650 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "C" Number of atoms: 6649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6649 Classifications: {'peptide': 843} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 793} Chain: "D" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1170 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "I" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1521 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 922 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 2, 'TRANS': 132} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 147 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "Q" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1174 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "X" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 668 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Z" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 23} Chain: "r" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 728 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "s" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 600 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'TRANS': 72} Chain: "L" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2853 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3415 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 413} Chain breaks: 1 Chain: "N" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 4613 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 459} Link IDs: {'PTRANS': 36, 'TRANS': 754} Chain breaks: 3 Unresolved non-hydrogen bonds: 1794 Unresolved non-hydrogen angles: 2275 Unresolved non-hydrogen dihedrals: 1525 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 22, 'TRP:plan': 19, 'ASP:plan': 21, 'PHE:plan': 12, 'GLU:plan': 59, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1055 Chain: "A" Number of atoms: 17494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2234, 17494 Classifications: {'peptide': 2234} Incomplete info: {'backbone_only': 235} Link IDs: {'PCIS': 2, 'PTRANS': 125, 'TRANS': 2106} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1088 Unresolved non-hydrogen angles: 1575 Unresolved non-hydrogen dihedrals: 742 Unresolved non-hydrogen chiralities: 298 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 10, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'HIS:plan': 12, 'PHE:plan': 8, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 542 Chain: "S" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1386 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain breaks: 4 Chain: "T" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 2268 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 7, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 1285 Unresolved non-hydrogen angles: 1589 Unresolved non-hydrogen dihedrals: 1099 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 8, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 20, 'GLU:plan': 42, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 747 Chain: "4" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1610 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 26, 'rna3p_pyr': 28} Link IDs: {'rna2p': 21, 'rna3p': 54} Chain breaks: 1 Chain: "J" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2026 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain breaks: 3 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 21.56, per 1000 atoms: 0.39 Number of scatterers: 55463 At special positions: 0 Unit cell: (247.08, 228.52, 223.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 206 16.00 P 300 15.00 O 11231 8.00 N 9963 7.00 C 33763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS r 82 " - pdb=" SG CYS r 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A1194 " - pdb=" SG CYS A1228 " distance=2.04 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: 17.13 Conformation dependent library (CDL) restraints added in 7.1 seconds 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12030 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 47 sheets defined 52.2% alpha, 10.3% beta 77 base pairs and 136 stacking pairs defined. Time for finding SS restraints: 15.32 Creating SS restraints... Processing helix chain '7' and resid 421 through 432 removed outlier: 4.337A pdb=" N GLN 7 426 " --> pdb=" O ALA 7 422 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU 7 427 " --> pdb=" O SER 7 423 " (cutoff:3.500A) Processing helix chain '7' and resid 435 through 450 removed outlier: 3.918A pdb=" N LEU 7 439 " --> pdb=" O ASP 7 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU 7 440 " --> pdb=" O PRO 7 436 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 472 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.685A pdb=" N ASP C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 270 through 292 Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.660A pdb=" N LYS C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.959A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 646 Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 755 through 761 removed outlier: 4.097A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 777 Processing helix chain 'C' and resid 804 through 822 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 841 No H-bonds generated for 'chain 'C' and resid 839 through 841' Processing helix chain 'C' and resid 842 through 853 removed outlier: 3.539A pdb=" N VAL C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 880 No H-bonds generated for 'chain 'C' and resid 878 through 880' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 942 removed outlier: 4.307A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG C 931 " --> pdb=" O PRO C 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 35 through 50 removed outlier: 3.558A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 removed outlier: 4.410A pdb=" N MET D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.870A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 15 Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 22 through 31 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 43 through 53 removed outlier: 3.856A pdb=" N VAL I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 96 through 111 Processing helix chain 'I' and resid 112 through 121 Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.621A pdb=" N ASN I 125 " --> pdb=" O PRO I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 154 Processing helix chain 'I' and resid 167 through 174 removed outlier: 3.598A pdb=" N LEU I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 314 removed outlier: 4.923A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 358 removed outlier: 3.902A pdb=" N ARG K 358 " --> pdb=" O VAL K 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 32 Processing helix chain 'M' and resid 38 through 47 Processing helix chain 'M' and resid 62 through 66 removed outlier: 3.635A pdb=" N ILE M 65 " --> pdb=" O PRO M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 77 removed outlier: 3.766A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 3.646A pdb=" N LEU M 89 " --> pdb=" O SER M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 124 Processing helix chain 'Q' and resid 14 through 34 removed outlier: 3.943A pdb=" N ILE Q 18 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 43 through 45 No H-bonds generated for 'chain 'Q' and resid 43 through 45' Processing helix chain 'Q' and resid 46 through 65 removed outlier: 3.787A pdb=" N PHE Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 81 Processing helix chain 'Q' and resid 85 through 93 Processing helix chain 'Q' and resid 102 through 111 removed outlier: 6.451A pdb=" N THR Q 108 " --> pdb=" O CYS Q 105 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG Q 109 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 121 Processing helix chain 'X' and resid 23 through 32 Processing helix chain 'X' and resid 33 through 81 removed outlier: 4.177A pdb=" N LYS X 81 " --> pdb=" O GLN X 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 91 through 100 Processing helix chain 'r' and resid 101 through 108 Processing helix chain 'r' and resid 118 through 133 Processing helix chain 's' and resid 23 through 36 Processing helix chain 's' and resid 38 through 40 No H-bonds generated for 'chain 's' and resid 38 through 40' Processing helix chain 'L' and resid 54 through 78 Processing helix chain 'L' and resid 88 through 119 removed outlier: 4.257A pdb=" N VAL L 92 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 153 through 158 Processing helix chain 'L' and resid 160 through 172 Processing helix chain 'L' and resid 180 through 211 Processing helix chain 'L' and resid 211 through 216 Processing helix chain 'L' and resid 216 through 223 Processing helix chain 'L' and resid 225 through 236 Processing helix chain 'L' and resid 237 through 243 removed outlier: 3.677A pdb=" N LYS L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 250 Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 287 through 307 Processing helix chain 'L' and resid 314 through 333 Processing helix chain 'L' and resid 356 through 367 Processing helix chain 'L' and resid 369 through 376 Processing helix chain 'L' and resid 413 through 417 Processing helix chain 'L' and resid 421 through 431 Processing helix chain 'F' and resid 82 through 97 Processing helix chain 'F' and resid 104 through 115 removed outlier: 3.643A pdb=" N LEU F 115 " --> pdb=" O CYS F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 143 through 152 removed outlier: 3.613A pdb=" N THR F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 202 Proline residue: F 187 - end of helix Processing helix chain 'F' and resid 203 through 220 Processing helix chain 'N' and resid 137 through 141 Processing helix chain 'N' and resid 142 through 149 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE N 160 " --> pdb=" O GLU N 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 155 through 160' Processing helix chain 'N' and resid 168 through 173 Processing helix chain 'N' and resid 183 through 193 removed outlier: 4.193A pdb=" N PHE N 187 " --> pdb=" O PRO N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 305 Processing helix chain 'N' and resid 308 through 322 removed outlier: 3.542A pdb=" N TRP N 312 " --> pdb=" O HIS N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 339 Processing helix chain 'N' and resid 343 through 353 removed outlier: 3.873A pdb=" N ARG N 351 " --> pdb=" O LEU N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 369 removed outlier: 3.563A pdb=" N ALA N 358 " --> pdb=" O PRO N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 383 Processing helix chain 'N' and resid 385 through 398 removed outlier: 4.554A pdb=" N ARG N 391 " --> pdb=" O ARG N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 403 through 412 Processing helix chain 'N' and resid 415 through 428 Processing helix chain 'N' and resid 433 through 442 removed outlier: 3.530A pdb=" N ARG N 442 " --> pdb=" O LEU N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 459 Processing helix chain 'N' and resid 465 through 477 Processing helix chain 'N' and resid 479 through 497 removed outlier: 3.570A pdb=" N ARG N 495 " --> pdb=" O ILE N 491 " (cutoff:3.500A) Processing helix chain 'N' and resid 502 through 516 Processing helix chain 'N' and resid 518 through 532 removed outlier: 3.981A pdb=" N CYS N 522 " --> pdb=" O SER N 518 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 552 Processing helix chain 'N' and resid 556 through 568 removed outlier: 3.690A pdb=" N GLN N 568 " --> pdb=" O ALA N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 574 through 587 Processing helix chain 'N' and resid 590 through 602 Processing helix chain 'N' and resid 610 through 620 removed outlier: 3.717A pdb=" N GLY N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) Processing helix chain 'N' and resid 623 through 637 removed outlier: 4.218A pdb=" N ALA N 637 " --> pdb=" O LEU N 633 " (cutoff:3.500A) Processing helix chain 'N' and resid 642 through 654 removed outlier: 3.606A pdb=" N GLU N 654 " --> pdb=" O LYS N 650 " (cutoff:3.500A) Processing helix chain 'N' and resid 657 through 670 Processing helix chain 'N' and resid 674 through 686 Processing helix chain 'N' and resid 690 through 705 removed outlier: 3.723A pdb=" N ALA N 694 " --> pdb=" O ASN N 690 " (cutoff:3.500A) Processing helix chain 'N' and resid 708 through 722 removed outlier: 3.715A pdb=" N LYS N 722 " --> pdb=" O ILE N 718 " (cutoff:3.500A) Processing helix chain 'N' and resid 724 through 739 Processing helix chain 'N' and resid 745 through 756 Processing helix chain 'N' and resid 758 through 773 removed outlier: 3.967A pdb=" N ALA N 762 " --> pdb=" O GLN N 758 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN N 773 " --> pdb=" O SER N 769 " (cutoff:3.500A) Processing helix chain 'N' and resid 778 through 786 removed outlier: 4.083A pdb=" N GLU N 782 " --> pdb=" O GLY N 778 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 806 Processing helix chain 'N' and resid 810 through 820 Processing helix chain 'N' and resid 827 through 837 removed outlier: 4.116A pdb=" N CYS N 837 " --> pdb=" O ALA N 833 " (cutoff:3.500A) Processing helix chain 'N' and resid 843 through 854 Processing helix chain 'N' and resid 856 through 870 removed outlier: 3.792A pdb=" N ILE N 870 " --> pdb=" O ARG N 866 " (cutoff:3.500A) Processing helix chain 'N' and resid 875 through 888 Processing helix chain 'N' and resid 892 through 903 Processing helix chain 'N' and resid 908 through 919 removed outlier: 3.507A pdb=" N VAL N 915 " --> pdb=" O LEU N 911 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS N 917 " --> pdb=" O CYS N 913 " (cutoff:3.500A) Processing helix chain 'N' and resid 925 through 929 Processing helix chain 'N' and resid 934 through 940 removed outlier: 4.141A pdb=" N LYS N 938 " --> pdb=" O ALA N 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.820A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.888A pdb=" N HIS A 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.658A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.870A pdb=" N ASP A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.093A pdb=" N TYR A 254 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.595A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.668A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.603A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.558A pdb=" N SER A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.954A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.525A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.691A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.570A pdb=" N ILE A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.573A pdb=" N LEU A 838 " --> pdb=" O HIS A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.563A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 998 Processing helix chain 'A' and resid 1002 through 1014 removed outlier: 3.540A pdb=" N ASN A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1063 removed outlier: 6.670A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 3.810A pdb=" N ARG A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.525A pdb=" N ASN A1148 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 removed outlier: 3.506A pdb=" N ALA A1250 " --> pdb=" O GLN A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 3.974A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 removed outlier: 3.584A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1368 through 1372 Processing helix chain 'A' and resid 1374 through 1399 Processing helix chain 'A' and resid 1418 through 1424 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1486 removed outlier: 3.783A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1513 Processing helix chain 'A' and resid 1514 through 1516 No H-bonds generated for 'chain 'A' and resid 1514 through 1516' Processing helix chain 'A' and resid 1519 through 1525 Processing helix chain 'A' and resid 1528 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 removed outlier: 3.627A pdb=" N ILE A1571 " --> pdb=" O PRO A1567 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.667A pdb=" N THR A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 3.839A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1768 through 1773 removed outlier: 3.783A pdb=" N SER A1773 " --> pdb=" O GLU A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1833 through 1850 removed outlier: 3.509A pdb=" N ARG A1850 " --> pdb=" O ALA A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 Processing helix chain 'A' and resid 1894 through 1898 removed outlier: 3.691A pdb=" N LEU A1897 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1907 Processing helix chain 'A' and resid 1922 through 1926 Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1948 through 1954 Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.616A pdb=" N LYS A1978 " --> pdb=" O GLU A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2002 Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'A' and resid 2072 through 2081 Processing helix chain 'A' and resid 2083 through 2087 Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2189 through 2203 Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2254 No H-bonds generated for 'chain 'A' and resid 2252 through 2254' Processing helix chain 'A' and resid 2310 through 2316 removed outlier: 3.789A pdb=" N HIS A2313 " --> pdb=" O ARG A2310 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A2316 " --> pdb=" O HIS A2313 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 184 Processing helix chain 'S' and resid 200 through 219 Processing helix chain 'S' and resid 251 through 255 removed outlier: 3.527A pdb=" N LEU S 254 " --> pdb=" O ALA S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 Processing helix chain 'S' and resid 291 through 309 Processing helix chain 'S' and resid 334 through 336 No H-bonds generated for 'chain 'S' and resid 334 through 336' Processing helix chain 'S' and resid 337 through 343 Processing helix chain 'S' and resid 352 through 356 removed outlier: 3.633A pdb=" N THR S 356 " --> pdb=" O GLN S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 375 Processing helix chain 'T' and resid 658 through 673 removed outlier: 3.614A pdb=" N ARG T 673 " --> pdb=" O MET T 669 " (cutoff:3.500A) Processing helix chain 'T' and resid 680 through 689 removed outlier: 5.283A pdb=" N HIS T 686 " --> pdb=" O GLU T 682 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS T 687 " --> pdb=" O LYS T 683 " (cutoff:3.500A) Processing helix chain 'T' and resid 691 through 696 removed outlier: 3.917A pdb=" N LEU T 695 " --> pdb=" O ASP T 691 " (cutoff:3.500A) Processing helix chain 'T' and resid 700 through 738 removed outlier: 3.573A pdb=" N GLU T 738 " --> pdb=" O LYS T 734 " (cutoff:3.500A) Processing helix chain 'T' and resid 746 through 753 removed outlier: 3.584A pdb=" N LYS T 753 " --> pdb=" O GLU T 749 " (cutoff:3.500A) Processing helix chain 'T' and resid 757 through 762 Processing helix chain 'T' and resid 765 through 805 removed outlier: 3.789A pdb=" N ARG T 769 " --> pdb=" O LYS T 765 " (cutoff:3.500A) Processing helix chain 'T' and resid 813 through 821 Processing helix chain 'T' and resid 824 through 830 removed outlier: 4.111A pdb=" N VAL T 830 " --> pdb=" O ARG T 826 " (cutoff:3.500A) Processing helix chain 'T' and resid 832 through 845 Processing helix chain 'T' and resid 857 through 911 removed outlier: 3.584A pdb=" N GLU T 890 " --> pdb=" O GLU T 886 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 923 Processing helix chain 'T' and resid 924 through 928 removed outlier: 4.105A pdb=" N LYS T 927 " --> pdb=" O THR T 924 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP T 928 " --> pdb=" O LEU T 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 924 through 928' Processing helix chain 'T' and resid 929 through 935 removed outlier: 4.260A pdb=" N GLU T 932 " --> pdb=" O HIS T 929 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY T 934 " --> pdb=" O TRP T 931 " (cutoff:3.500A) Processing helix chain 'T' and resid 938 through 965 Processing helix chain 'T' and resid 976 through 984 removed outlier: 3.869A pdb=" N LYS T 982 " --> pdb=" O LYS T 978 " (cutoff:3.500A) Processing helix chain 'T' and resid 987 through 994 Processing helix chain 'T' and resid 996 through 1024 removed outlier: 3.574A pdb=" N LYS T1000 " --> pdb=" O SER T 996 " (cutoff:3.500A) Processing helix chain 'T' and resid 1033 through 1040 Processing helix chain 'T' and resid 1041 through 1052 Processing helix chain 'T' and resid 1055 through 1061 Processing helix chain 'T' and resid 1063 through 1078 Processing helix chain 'J' and resid 388 through 395 Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'J' and resid 480 through 485 Processing helix chain 'J' and resid 485 through 492 Processing helix chain 'J' and resid 492 through 519 removed outlier: 3.693A pdb=" N ARG J 518 " --> pdb=" O ALA J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 535 removed outlier: 3.705A pdb=" N GLU J 535 " --> pdb=" O LYS J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 553 through 567 Processing helix chain 'J' and resid 587 through 601 Processing helix chain 'J' and resid 653 through 665 removed outlier: 4.119A pdb=" N ALA J 657 " --> pdb=" O THR J 653 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS J 664 " --> pdb=" O HIS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 683 removed outlier: 4.125A pdb=" N TRP J 670 " --> pdb=" O ALA J 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 191 removed outlier: 6.478A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AA3, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.351A pdb=" N MET C 475 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AA5, first strand: chain 'C' and resid 618 through 621 removed outlier: 4.021A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 618 through 621 removed outlier: 4.021A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.499A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 663 through 666 removed outlier: 7.051A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 896 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.170A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'I' and resid 57 through 58 removed outlier: 7.118A pdb=" N VAL I 57 " --> pdb=" O GLN I 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'I' and resid 156 through 157 Processing sheet with id=AB6, first strand: chain 'M' and resid 35 through 37 removed outlier: 9.473A pdb=" N VAL M 81 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE M 54 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL M 83 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET M 56 " --> pdb=" O VAL M 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'r' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain 'r' and resid 80 through 82 removed outlier: 3.564A pdb=" N CYS r 87 " --> pdb=" O CYS r 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 14 through 18 removed outlier: 8.657A pdb=" N LEU s 68 " --> pdb=" O GLU s 3 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL s 5 " --> pdb=" O LEU s 68 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU s 70 " --> pdb=" O VAL s 5 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN s 7 " --> pdb=" O LEU s 70 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N TYR s 72 " --> pdb=" O ASN s 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 377 through 379 removed outlier: 3.503A pdb=" N MET L 378 " --> pdb=" O TRP A1503 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 168 through 169 Processing sheet with id=AC4, first strand: chain 'F' and resid 221 through 228 removed outlier: 5.262A pdb=" N ASN F 223 " --> pdb=" O MET F 520 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET F 520 " --> pdb=" O ASN F 223 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 234 through 239 removed outlier: 3.564A pdb=" N TYR F 236 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS F 255 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR F 268 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU F 257 " --> pdb=" O LEU F 266 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 276 through 281 removed outlier: 3.669A pdb=" N ALA F 278 " --> pdb=" O CYS F 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 317 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 326 through 331 removed outlier: 3.895A pdb=" N ARG F 328 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP F 351 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 368 through 373 removed outlier: 6.483A pdb=" N GLY F 389 " --> pdb=" O PHE F 402 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F 402 " --> pdb=" O GLY F 389 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 391 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 398 " --> pdb=" O ASP F 393 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 410 through 415 removed outlier: 6.002A pdb=" N CYS F 431 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR F 444 " --> pdb=" O CYS F 431 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL F 433 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 452 through 457 removed outlier: 3.808A pdb=" N GLY F 454 " --> pdb=" O GLY F 468 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR F 473 " --> pdb=" O ALA F 469 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA F 474 " --> pdb=" O THR F 487 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR F 487 " --> pdb=" O ALA F 474 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 476 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AD4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AD5, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AD6, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AD7, first strand: chain 'A' and resid 905 through 910 Processing sheet with id=AD8, first strand: chain 'A' and resid 1085 through 1091 removed outlier: 6.552A pdb=" N PHE A1098 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A1088 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS A1096 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A1090 " --> pdb=" O ARG A1094 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1185 through 1188 removed outlier: 3.678A pdb=" N ALA A1226 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1334 through 1335 removed outlier: 4.235A pdb=" N GLN A1363 " --> pdb=" O ILE A1335 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1341 through 1346 removed outlier: 3.502A pdb=" N GLY A1349 " --> pdb=" O THR A1346 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AE4, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 7.812A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1762 through 1763 removed outlier: 6.365A pdb=" N ILE A1861 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER A1887 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A1810 " --> pdb=" O PHE A1779 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A1818 " --> pdb=" O ILE A1809 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1798 through 1803 removed outlier: 3.731A pdb=" N HIS A1791 " --> pdb=" O THR A1799 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR S 258 " --> pdb=" O LEU S 289 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 2091 through 2092 removed outlier: 5.933A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 2091 through 2092 removed outlier: 5.933A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A2124 " --> pdb=" O THR A2180 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A2145 " --> pdb=" O MET A2272 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 2140 through 2141 removed outlier: 3.593A pdb=" N ILE A2105 " --> pdb=" O LYS A2140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 2151 through 2152 Processing sheet with id=AF2, first strand: chain 'J' and resid 630 through 638 removed outlier: 5.423A pdb=" N LEU J 632 " --> pdb=" O ARG J 547 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG J 547 " --> pdb=" O LEU J 632 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS J 647 " --> pdb=" O GLY J 571 " (cutoff:3.500A) 2652 hydrogen bonds defined for protein. 7623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 192 hydrogen bonds 340 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 136 stacking parallelities Total time for adding SS restraints: 34.99 Time building geometry restraints manager: 18.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17366 1.34 - 1.46: 13838 1.46 - 1.58: 25041 1.58 - 1.71: 598 1.71 - 1.83: 329 Bond restraints: 57172 Sorted by residual: bond pdb=" CG PRO 7 421 " pdb=" CD PRO 7 421 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.46e+01 bond pdb=" N PRO 7 421 " pdb=" CD PRO 7 421 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" CB PRO 7 421 " pdb=" CG PRO 7 421 " ideal model delta sigma weight residual 1.492 1.687 -0.195 5.00e-02 4.00e+02 1.52e+01 bond pdb=" CB PRO N 270 " pdb=" CG PRO N 270 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.01e+00 bond pdb=" N PRO 7 421 " pdb=" CA PRO 7 421 " ideal model delta sigma weight residual 1.469 1.433 0.035 1.28e-02 6.10e+03 7.62e+00 ... (remaining 57167 not shown) Histogram of bond angle deviations from ideal: 90.53 - 99.34: 16 99.34 - 108.15: 4969 108.15 - 116.96: 36462 116.96 - 125.77: 35656 125.77 - 134.58: 1764 Bond angle restraints: 78867 Sorted by residual: angle pdb=" CA PRO 7 421 " pdb=" N PRO 7 421 " pdb=" CD PRO 7 421 " ideal model delta sigma weight residual 112.00 92.30 19.70 1.40e+00 5.10e-01 1.98e+02 angle pdb=" CA PRO N 270 " pdb=" N PRO N 270 " pdb=" CD PRO N 270 " ideal model delta sigma weight residual 112.00 92.79 19.21 1.40e+00 5.10e-01 1.88e+02 angle pdb=" N PRO 7 421 " pdb=" CD PRO 7 421 " pdb=" CG PRO 7 421 " ideal model delta sigma weight residual 103.20 90.53 12.67 1.50e+00 4.44e-01 7.13e+01 angle pdb=" CA PRO A1853 " pdb=" N PRO A1853 " pdb=" CD PRO A1853 " ideal model delta sigma weight residual 112.00 101.31 10.69 1.40e+00 5.10e-01 5.83e+01 angle pdb=" N PRO N 270 " pdb=" CD PRO N 270 " pdb=" CG PRO N 270 " ideal model delta sigma weight residual 103.20 94.02 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 78862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 33235 35.98 - 71.95: 1309 71.95 - 107.93: 128 107.93 - 143.90: 3 143.90 - 179.88: 12 Dihedral angle restraints: 34687 sinusoidal: 15940 harmonic: 18747 Sorted by residual: dihedral pdb=" CB CYS A1194 " pdb=" SG CYS A1194 " pdb=" SG CYS A1228 " pdb=" CB CYS A1228 " ideal model delta sinusoidal sigma weight residual 93.00 -177.41 -89.59 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" O4' C 5 68 " pdb=" C1' C 5 68 " pdb=" N1 C 5 68 " pdb=" C2 C 5 68 " ideal model delta sinusoidal sigma weight residual 200.00 59.77 140.23 1 1.50e+01 4.44e-03 7.55e+01 dihedral pdb=" O4' U 5 80 " pdb=" C1' U 5 80 " pdb=" N1 U 5 80 " pdb=" C2 U 5 80 " ideal model delta sinusoidal sigma weight residual -128.00 51.88 -179.88 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 34684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 8405 0.080 - 0.160: 567 0.160 - 0.240: 10 0.240 - 0.320: 1 0.320 - 0.399: 2 Chirality restraints: 8985 Sorted by residual: chirality pdb=" C1' A Z 72 " pdb=" O4' A Z 72 " pdb=" C2' A Z 72 " pdb=" N9 A Z 72 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C1' C Z 71 " pdb=" O4' C Z 71 " pdb=" C2' C Z 71 " pdb=" N1 C Z 71 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA PRO 7 421 " pdb=" N PRO 7 421 " pdb=" C PRO 7 421 " pdb=" CB PRO 7 421 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 8982 not shown) Planarity restraints: 9219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP N 269 " -0.134 5.00e-02 4.00e+02 1.82e-01 5.29e+01 pdb=" N PRO N 270 " 0.313 5.00e-02 4.00e+02 pdb=" CA PRO N 270 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO N 270 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 7 420 " 0.102 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO 7 421 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO 7 421 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO 7 421 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A Z 72 " -0.049 2.00e-02 2.50e+03 2.31e-02 1.47e+01 pdb=" N9 A Z 72 " 0.057 2.00e-02 2.50e+03 pdb=" C8 A Z 72 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A Z 72 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A Z 72 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A Z 72 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A Z 72 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A Z 72 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A Z 72 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A Z 72 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A Z 72 " 0.005 2.00e-02 2.50e+03 ... (remaining 9216 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 527 2.59 - 3.16: 45353 3.16 - 3.74: 91601 3.74 - 4.32: 122865 4.32 - 4.90: 196926 Nonbonded interactions: 457272 Sorted by model distance: nonbonded pdb=" O2' U 6 40 " pdb=" OD1 ASP r 91 " model vdw 2.007 2.440 nonbonded pdb=" OG1 THR 7 474 " pdb=" OG1 THR 7 482 " model vdw 2.106 2.440 nonbonded pdb=" OD2 ASP C 261 " pdb=" OG SER C 311 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR C 614 " pdb=" OD2 ASP C 643 " model vdw 2.141 2.440 nonbonded pdb=" OG SER N 32 " pdb=" O LYS A 537 " model vdw 2.149 2.440 ... (remaining 457267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 5.540 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 28.510 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 138.730 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.227 57172 Z= 0.263 Angle : 0.646 19.695 78867 Z= 0.362 Chirality : 0.041 0.399 8985 Planarity : 0.005 0.182 9219 Dihedral : 17.569 179.877 22648 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.53 % Favored : 94.41 % Rotamer: Outliers : 0.53 % Allowed : 13.10 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.11), residues: 6497 helix: 1.13 (0.09), residues: 3111 sheet: -0.73 (0.19), residues: 688 loop : -1.37 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 772 HIS 0.012 0.001 HIS A1791 PHE 0.023 0.002 PHE J 643 TYR 0.019 0.002 TYR A1991 ARG 0.010 0.001 ARG C 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 525 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 569 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6863 (pmt-80) REVERT: K 366 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7241 (mm-30) REVERT: L 431 GLN cc_start: 0.6200 (tm-30) cc_final: 0.5937 (tm-30) REVERT: N 145 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (mm) REVERT: T 895 LYS cc_start: 0.8604 (mmmt) cc_final: 0.7893 (mttt) outliers start: 25 outliers final: 12 residues processed: 541 average time/residue: 0.5628 time to fit residues: 503.0220 Evaluate side-chains 515 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 501 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 369 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 300 SER Chi-restraints excluded: chain N residue 374 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain S residue 252 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 574 optimal weight: 30.0000 chunk 515 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 275 optimal weight: 0.7980 chunk 532 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 396 optimal weight: 0.7980 chunk 617 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 112 ASN X 35 ASN L 144 ASN L 339 GLN ** F 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 GLN N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 737 ASN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 57172 Z= 0.316 Angle : 0.597 9.443 78867 Z= 0.309 Chirality : 0.042 0.418 8985 Planarity : 0.005 0.084 9219 Dihedral : 17.428 179.980 11706 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.67 % Allowed : 12.76 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 6497 helix: 1.29 (0.09), residues: 3160 sheet: -0.60 (0.20), residues: 684 loop : -1.32 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 772 HIS 0.008 0.001 HIS A1791 PHE 0.019 0.002 PHE A1311 TYR 0.018 0.002 TYR F 420 ARG 0.006 0.001 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 534 time to evaluate : 5.265 Fit side-chains revert: symmetry clash REVERT: I 142 MET cc_start: 0.8449 (mtm) cc_final: 0.8201 (mtm) REVERT: M 121 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: Q 76 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: r 66 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8612 (mp) REVERT: L 431 GLN cc_start: 0.6482 (tm-30) cc_final: 0.6176 (tm-30) REVERT: N 34 ILE cc_start: 0.3973 (mm) cc_final: 0.3742 (mm) REVERT: N 382 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6423 (pp) REVERT: A 1270 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 1762 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5753 (t80) REVERT: S 293 ASN cc_start: 0.8247 (m-40) cc_final: 0.8042 (m-40) REVERT: T 881 SER cc_start: 0.8433 (m) cc_final: 0.7862 (p) REVERT: T 895 LYS cc_start: 0.8571 (mmmt) cc_final: 0.7918 (mttt) outliers start: 126 outliers final: 73 residues processed: 626 average time/residue: 0.5848 time to fit residues: 618.7914 Evaluate side-chains 581 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 502 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 460 LEU Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 21 ASP Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 369 THR Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 276 ASP Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 374 ARG Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1789 THR Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 859 LEU Chi-restraints excluded: chain T residue 883 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 343 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 513 optimal weight: 0.9980 chunk 420 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 618 optimal weight: 20.0000 chunk 668 optimal weight: 5.9990 chunk 550 optimal weight: 2.9990 chunk 613 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 496 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN M 34 GLN Q 37 HIS Q 55 GLN Q 112 ASN X 35 ASN r 100 ASN s 34 GLN L 175 GLN ** F 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 GLN N 368 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN A 461 HIS A 483 GLN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 57172 Z= 0.367 Angle : 0.621 10.639 78867 Z= 0.321 Chirality : 0.043 0.440 8985 Planarity : 0.005 0.067 9219 Dihedral : 17.389 179.703 11686 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 3.77 % Allowed : 13.05 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 6497 helix: 1.28 (0.09), residues: 3179 sheet: -0.56 (0.20), residues: 693 loop : -1.34 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 519 HIS 0.008 0.001 HIS N 368 PHE 0.024 0.002 PHE C 228 TYR 0.019 0.002 TYR A2062 ARG 0.007 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 535 time to evaluate : 4.579 Fit side-chains revert: symmetry clash REVERT: C 603 MET cc_start: 0.9069 (ttp) cc_final: 0.8755 (ttp) REVERT: C 949 ILE cc_start: 0.5209 (OUTLIER) cc_final: 0.4887 (tp) REVERT: D 88 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: K 393 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7794 (p90) REVERT: M 121 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: Q 76 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: r 66 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8636 (mp) REVERT: N 191 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7902 (pp) REVERT: N 382 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6401 (pp) REVERT: A 834 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7695 (p90) REVERT: A 1762 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5808 (t80) REVERT: A 1965 HIS cc_start: 0.7515 (t70) cc_final: 0.6967 (t70) REVERT: S 215 ASP cc_start: 0.6571 (m-30) cc_final: 0.6079 (t0) REVERT: S 253 ASP cc_start: 0.6315 (m-30) cc_final: 0.5971 (m-30) REVERT: T 895 LYS cc_start: 0.8550 (mmmt) cc_final: 0.7898 (mtmt) REVERT: J 492 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7316 (p0) outliers start: 178 outliers final: 117 residues processed: 668 average time/residue: 0.5521 time to fit residues: 618.5872 Evaluate side-chains 632 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 504 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 460 LEU Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 56 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 21 ASP Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 369 THR Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 429 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 300 SER Chi-restraints excluded: chain N residue 321 VAL Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 374 ARG Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1788 VAL Chi-restraints excluded: chain A residue 1789 THR Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1896 CYS Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain T residue 859 LEU Chi-restraints excluded: chain T residue 865 ILE Chi-restraints excluded: chain T residue 883 GLN Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 536 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 611 optimal weight: 5.9990 chunk 465 optimal weight: 0.0470 chunk 321 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 415 optimal weight: 0.7980 chunk 620 optimal weight: 6.9990 chunk 657 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 588 optimal weight: 40.0000 chunk 177 optimal weight: 4.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN M 120 GLN Q 55 GLN X 39 ASN s 34 GLN ** F 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1424 GLN A1599 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 57172 Z= 0.241 Angle : 0.557 11.395 78867 Z= 0.287 Chirality : 0.041 0.410 8985 Planarity : 0.004 0.058 9219 Dihedral : 17.311 179.814 11686 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 3.12 % Allowed : 14.09 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.28 (0.11), residues: 6497 helix: 1.49 (0.09), residues: 3185 sheet: -0.52 (0.20), residues: 690 loop : -1.26 (0.13), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 772 HIS 0.007 0.001 HIS A1791 PHE 0.026 0.001 PHE A1772 TYR 0.017 0.002 TYR A1620 ARG 0.006 0.000 ARG N 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 533 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 424 LYS cc_start: 0.6614 (mtmm) cc_final: 0.6308 (ptpp) REVERT: 7 472 ARG cc_start: 0.7407 (mmt-90) cc_final: 0.7152 (mmt-90) REVERT: C 481 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7736 (mpp) REVERT: C 603 MET cc_start: 0.9013 (ttp) cc_final: 0.8672 (ttp) REVERT: C 772 TRP cc_start: 0.7268 (t60) cc_final: 0.7065 (t60) REVERT: D 15 ASP cc_start: 0.8141 (m-30) cc_final: 0.7938 (m-30) REVERT: D 88 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8381 (ttpt) REVERT: K 393 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7646 (p90) REVERT: M 121 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: Q 76 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: X 24 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6761 (ptt90) REVERT: r 66 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8626 (mp) REVERT: L 184 LEU cc_start: 0.8002 (tp) cc_final: 0.7502 (mp) REVERT: N 176 TYR cc_start: 0.8139 (t80) cc_final: 0.7926 (t80) REVERT: N 382 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6349 (pp) REVERT: A 984 MET cc_start: 0.8024 (ttm) cc_final: 0.7784 (ttm) REVERT: A 1762 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5821 (t80) REVERT: A 1965 HIS cc_start: 0.7667 (t70) cc_final: 0.7144 (t70) REVERT: S 148 GLU cc_start: 0.4145 (OUTLIER) cc_final: 0.1086 (mt-10) REVERT: S 215 ASP cc_start: 0.6560 (m-30) cc_final: 0.6051 (t0) REVERT: S 253 ASP cc_start: 0.6192 (m-30) cc_final: 0.5807 (m-30) REVERT: S 264 ASP cc_start: 0.7461 (p0) cc_final: 0.7159 (p0) REVERT: S 296 ASP cc_start: 0.7954 (t0) cc_final: 0.7727 (p0) REVERT: T 862 GLN cc_start: 0.6906 (mm110) cc_final: 0.6219 (tp-100) REVERT: T 881 SER cc_start: 0.8646 (m) cc_final: 0.8051 (p) REVERT: T 895 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7901 (mttt) REVERT: J 492 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7295 (p0) outliers start: 147 outliers final: 94 residues processed: 641 average time/residue: 0.5541 time to fit residues: 592.9056 Evaluate side-chains 615 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 510 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 56 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 21 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 209 GLU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 420 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 276 ASP Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 300 SER Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1788 VAL Chi-restraints excluded: chain A residue 1789 THR Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain T residue 883 GLN Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 536 ASP Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 547 optimal weight: 0.9980 chunk 373 optimal weight: 0.7980 chunk 9 optimal weight: 40.0000 chunk 489 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 560 optimal weight: 1.9990 chunk 454 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 chunk 589 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 55 GLN s 34 GLN N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 57172 Z= 0.197 Angle : 0.534 12.224 78867 Z= 0.275 Chirality : 0.040 0.397 8985 Planarity : 0.004 0.057 9219 Dihedral : 17.242 179.836 11681 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 3.58 % Allowed : 14.13 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 6497 helix: 1.66 (0.09), residues: 3179 sheet: -0.45 (0.20), residues: 693 loop : -1.19 (0.13), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 637 HIS 0.038 0.001 HIS A 97 PHE 0.031 0.001 PHE A1772 TYR 0.016 0.001 TYR A1620 ARG 0.006 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 534 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 472 ARG cc_start: 0.7421 (mmt-90) cc_final: 0.7174 (mmt-90) REVERT: C 481 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7890 (mpp) REVERT: C 603 MET cc_start: 0.8996 (ttp) cc_final: 0.8653 (ttp) REVERT: C 949 ILE cc_start: 0.5241 (OUTLIER) cc_final: 0.4994 (tp) REVERT: D 15 ASP cc_start: 0.8147 (m-30) cc_final: 0.7945 (m-30) REVERT: D 88 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (ttpt) REVERT: K 393 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7555 (p90) REVERT: M 28 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: M 121 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: Q 76 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: X 24 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6843 (ptm-80) REVERT: r 66 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8618 (mp) REVERT: s 46 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7701 (mptp) REVERT: L 184 LEU cc_start: 0.7974 (tp) cc_final: 0.7487 (mp) REVERT: N 176 TYR cc_start: 0.7979 (t80) cc_final: 0.7728 (t80) REVERT: N 339 CYS cc_start: 0.7484 (t) cc_final: 0.6812 (p) REVERT: N 382 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6283 (pp) REVERT: A 984 MET cc_start: 0.8053 (ttm) cc_final: 0.7807 (ttm) REVERT: A 1419 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 1762 TYR cc_start: 0.6158 (OUTLIER) cc_final: 0.5801 (t80) REVERT: A 1965 HIS cc_start: 0.7693 (t70) cc_final: 0.7102 (t70) REVERT: S 148 GLU cc_start: 0.4036 (OUTLIER) cc_final: 0.0479 (mm-30) REVERT: S 215 ASP cc_start: 0.6555 (m-30) cc_final: 0.6046 (t0) REVERT: S 253 ASP cc_start: 0.6356 (m-30) cc_final: 0.5979 (m-30) REVERT: S 264 ASP cc_start: 0.7462 (p0) cc_final: 0.7121 (p0) REVERT: T 862 GLN cc_start: 0.6832 (mm110) cc_final: 0.6165 (tp-100) REVERT: T 881 SER cc_start: 0.8646 (m) cc_final: 0.8054 (p) REVERT: T 895 LYS cc_start: 0.8531 (mmmt) cc_final: 0.7878 (mttt) REVERT: J 492 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7228 (p0) outliers start: 169 outliers final: 116 residues processed: 664 average time/residue: 0.5507 time to fit residues: 615.6145 Evaluate side-chains 643 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 512 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 56 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 10 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 21 ASP Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain L residue 420 ILE Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 273 TYR Chi-restraints excluded: chain N residue 276 ASP Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 300 SER Chi-restraints excluded: chain N residue 347 LEU Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 374 ARG Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1413 ASP Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1789 THR Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1896 CYS Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain T residue 883 GLN Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 536 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 221 optimal weight: 0.9990 chunk 591 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 657 optimal weight: 0.8980 chunk 546 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 345 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 55 GLN X 35 ASN N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS A 297 ASN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 57172 Z= 0.179 Angle : 0.523 12.111 78867 Z= 0.268 Chirality : 0.039 0.386 8985 Planarity : 0.004 0.056 9219 Dihedral : 17.181 179.923 11679 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.74 % Rotamer: Outliers : 3.56 % Allowed : 14.30 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.59 (0.11), residues: 6497 helix: 1.78 (0.09), residues: 3180 sheet: -0.41 (0.20), residues: 694 loop : -1.14 (0.13), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 750 HIS 0.009 0.001 HIS N 368 PHE 0.047 0.001 PHE A1772 TYR 0.017 0.001 TYR A1991 ARG 0.007 0.000 ARG r 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 546 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 472 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7107 (mmt-90) REVERT: C 481 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: C 603 MET cc_start: 0.8980 (ttp) cc_final: 0.8640 (ttp) REVERT: C 641 MET cc_start: 0.9110 (mmm) cc_final: 0.8684 (mmm) REVERT: C 949 ILE cc_start: 0.5206 (OUTLIER) cc_final: 0.4937 (tp) REVERT: D 15 ASP cc_start: 0.8161 (m-30) cc_final: 0.7959 (m-30) REVERT: D 88 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8422 (ttpt) REVERT: K 393 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7442 (p90) REVERT: M 28 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: Q 76 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: X 24 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6895 (ptm160) REVERT: X 46 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7234 (tp30) REVERT: r 66 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8595 (mp) REVERT: s 46 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7756 (mptp) REVERT: L 184 LEU cc_start: 0.7988 (tp) cc_final: 0.7499 (mp) REVERT: L 424 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8476 (tp) REVERT: N 176 TYR cc_start: 0.7923 (t80) cc_final: 0.7623 (t80) REVERT: N 191 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7753 (pp) REVERT: N 254 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6994 (mtp85) REVERT: N 339 CYS cc_start: 0.7452 (t) cc_final: 0.6778 (p) REVERT: N 382 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6262 (pp) REVERT: A 559 ASP cc_start: 0.8732 (m-30) cc_final: 0.8520 (t0) REVERT: A 690 MET cc_start: 0.8927 (mmm) cc_final: 0.8708 (mmm) REVERT: A 984 MET cc_start: 0.8079 (ttm) cc_final: 0.7846 (ttm) REVERT: A 1965 HIS cc_start: 0.7674 (t70) cc_final: 0.7034 (t70) REVERT: S 148 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.0969 (tt0) REVERT: S 215 ASP cc_start: 0.6543 (m-30) cc_final: 0.6034 (t0) REVERT: S 253 ASP cc_start: 0.6475 (m-30) cc_final: 0.6106 (m-30) REVERT: S 264 ASP cc_start: 0.7507 (p0) cc_final: 0.7178 (p0) REVERT: T 881 SER cc_start: 0.8650 (m) cc_final: 0.8059 (p) REVERT: T 895 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7878 (mttt) REVERT: J 492 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7219 (p0) outliers start: 168 outliers final: 119 residues processed: 670 average time/residue: 0.5710 time to fit residues: 641.9206 Evaluate side-chains 651 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 517 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 56 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 10 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 21 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain L residue 420 ILE Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 254 ARG Chi-restraints excluded: chain N residue 273 TYR Chi-restraints excluded: chain N residue 276 ASP Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 347 LEU Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 374 ARG Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1896 CYS Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain T residue 883 GLN Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 634 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 374 optimal weight: 0.7980 chunk 480 optimal weight: 5.9990 chunk 372 optimal weight: 0.7980 chunk 553 optimal weight: 8.9990 chunk 367 optimal weight: 0.0980 chunk 655 optimal weight: 20.0000 chunk 410 optimal weight: 2.9990 chunk 399 optimal weight: 0.0670 chunk 302 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 55 GLN X 35 ASN r 100 ASN ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 HIS ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 480 ASN J 508 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 57172 Z= 0.147 Angle : 0.507 12.115 78867 Z= 0.260 Chirality : 0.038 0.373 8985 Planarity : 0.004 0.072 9219 Dihedral : 17.116 179.697 11677 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.92 % Rotamer: Outliers : 2.75 % Allowed : 15.36 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.70 (0.11), residues: 6497 helix: 1.86 (0.09), residues: 3204 sheet: -0.34 (0.20), residues: 693 loop : -1.10 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 750 HIS 0.009 0.001 HIS N 368 PHE 0.023 0.001 PHE A1772 TYR 0.015 0.001 TYR A1620 ARG 0.011 0.000 ARG N 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 551 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 444 ARG cc_start: 0.6509 (ttp80) cc_final: 0.6156 (tmm160) REVERT: 7 472 ARG cc_start: 0.7407 (mmt-90) cc_final: 0.7123 (mmt-90) REVERT: C 603 MET cc_start: 0.8952 (ttp) cc_final: 0.8592 (ttp) REVERT: D 15 ASP cc_start: 0.8174 (m-30) cc_final: 0.7960 (m-30) REVERT: D 88 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8413 (ttpt) REVERT: K 366 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7358 (mm-30) REVERT: K 393 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7261 (p90) REVERT: M 28 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: Q 5 LYS cc_start: 0.5548 (mttt) cc_final: 0.4959 (tttp) REVERT: Q 76 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: Q 107 GLN cc_start: 0.7896 (tp40) cc_final: 0.7689 (tp40) REVERT: X 24 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6958 (ptm160) REVERT: X 46 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7256 (tp30) REVERT: r 66 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8536 (mp) REVERT: r 112 MET cc_start: 0.7140 (mmp) cc_final: 0.6403 (mmt) REVERT: s 46 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7916 (mptp) REVERT: L 184 LEU cc_start: 0.8066 (tp) cc_final: 0.7578 (mp) REVERT: L 232 MET cc_start: 0.8305 (ptp) cc_final: 0.8017 (mtm) REVERT: L 424 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8476 (tp) REVERT: L 431 GLN cc_start: 0.6517 (tm-30) cc_final: 0.6216 (tm-30) REVERT: N 176 TYR cc_start: 0.7945 (t80) cc_final: 0.7582 (t80) REVERT: N 191 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7654 (pp) REVERT: N 339 CYS cc_start: 0.7479 (t) cc_final: 0.6862 (p) REVERT: N 382 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6254 (pp) REVERT: A 559 ASP cc_start: 0.8637 (m-30) cc_final: 0.8436 (t0) REVERT: A 607 ASP cc_start: 0.8256 (m-30) cc_final: 0.7909 (m-30) REVERT: A 690 MET cc_start: 0.9004 (mmm) cc_final: 0.8784 (mmm) REVERT: A 984 MET cc_start: 0.8083 (ttm) cc_final: 0.7858 (ttm) REVERT: A 1965 HIS cc_start: 0.7675 (t70) cc_final: 0.7006 (t70) REVERT: S 148 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.0435 (mm-30) REVERT: S 215 ASP cc_start: 0.6538 (m-30) cc_final: 0.6048 (t0) REVERT: S 253 ASP cc_start: 0.6343 (m-30) cc_final: 0.5998 (m-30) REVERT: S 264 ASP cc_start: 0.7567 (p0) cc_final: 0.7128 (p0) REVERT: T 862 GLN cc_start: 0.6845 (mm110) cc_final: 0.6258 (tp-100) REVERT: T 881 SER cc_start: 0.8611 (m) cc_final: 0.8014 (p) REVERT: T 895 LYS cc_start: 0.8517 (mmmt) cc_final: 0.7891 (mttt) REVERT: J 492 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7255 (p0) outliers start: 130 outliers final: 89 residues processed: 647 average time/residue: 0.5623 time to fit residues: 609.6717 Evaluate side-chains 630 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 529 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 10 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 46 LYS Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain L residue 420 ILE Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 347 LEU Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 598 MET Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 405 optimal weight: 0.8980 chunk 261 optimal weight: 0.0980 chunk 391 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 416 optimal weight: 0.5980 chunk 446 optimal weight: 0.0870 chunk 324 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 515 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 ASN M 34 GLN Q 55 GLN X 35 ASN ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 HIS ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 775 ASN A 994 ASN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 GLN J 480 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 57172 Z= 0.137 Angle : 0.503 12.070 78867 Z= 0.256 Chirality : 0.038 0.362 8985 Planarity : 0.004 0.054 9219 Dihedral : 17.051 179.814 11677 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 2.33 % Allowed : 15.87 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.86 (0.11), residues: 6497 helix: 1.99 (0.09), residues: 3212 sheet: -0.28 (0.20), residues: 687 loop : -1.02 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 750 HIS 0.008 0.001 HIS N 368 PHE 0.029 0.001 PHE A1772 TYR 0.019 0.001 TYR A1991 ARG 0.008 0.000 ARG T 874 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 562 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 429 MET cc_start: 0.8794 (mmm) cc_final: 0.8535 (mmt) REVERT: 7 444 ARG cc_start: 0.6517 (ttp80) cc_final: 0.6201 (tmm160) REVERT: 7 472 ARG cc_start: 0.7400 (mmt-90) cc_final: 0.7112 (mmt-90) REVERT: C 603 MET cc_start: 0.8935 (ttp) cc_final: 0.8580 (ttp) REVERT: D 15 ASP cc_start: 0.8204 (m-30) cc_final: 0.8001 (m-30) REVERT: I 115 ASP cc_start: 0.7858 (m-30) cc_final: 0.7656 (m-30) REVERT: K 366 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7367 (mm-30) REVERT: K 393 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7062 (p90) REVERT: M 28 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: Q 5 LYS cc_start: 0.5523 (mttt) cc_final: 0.4998 (tttp) REVERT: Q 76 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: X 24 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6893 (ptm160) REVERT: r 66 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8490 (mp) REVERT: L 184 LEU cc_start: 0.8077 (tp) cc_final: 0.7604 (mp) REVERT: L 232 MET cc_start: 0.8277 (ptp) cc_final: 0.8074 (mtm) REVERT: L 424 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8484 (tp) REVERT: L 431 GLN cc_start: 0.6460 (tm-30) cc_final: 0.6175 (tm-30) REVERT: N 176 TYR cc_start: 0.7837 (t80) cc_final: 0.7413 (t80) REVERT: N 191 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7582 (pp) REVERT: N 339 CYS cc_start: 0.7576 (t) cc_final: 0.7131 (p) REVERT: N 382 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6477 (pp) REVERT: A 690 MET cc_start: 0.9055 (mmm) cc_final: 0.8840 (mmm) REVERT: A 984 MET cc_start: 0.8081 (ttm) cc_final: 0.7851 (ttm) REVERT: A 1416 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7233 (mm) REVERT: A 1965 HIS cc_start: 0.7669 (t70) cc_final: 0.6993 (t70) REVERT: S 148 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.0401 (mm-30) REVERT: S 215 ASP cc_start: 0.6521 (m-30) cc_final: 0.6020 (t0) REVERT: S 253 ASP cc_start: 0.6374 (m-30) cc_final: 0.6081 (m-30) REVERT: S 264 ASP cc_start: 0.7659 (p0) cc_final: 0.7240 (p0) REVERT: S 339 GLU cc_start: 0.6067 (mt-10) cc_final: 0.5856 (mt-10) REVERT: T 862 GLN cc_start: 0.6842 (mm110) cc_final: 0.6279 (tp-100) REVERT: T 881 SER cc_start: 0.8610 (m) cc_final: 0.8016 (p) REVERT: T 895 LYS cc_start: 0.8508 (mmmt) cc_final: 0.7892 (mttt) REVERT: J 492 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (p0) outliers start: 110 outliers final: 72 residues processed: 646 average time/residue: 0.5655 time to fit residues: 615.2221 Evaluate side-chains 614 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 531 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 136 ASN Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 10 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 347 LEU Chi-restraints excluded: chain N residue 356 ASP Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1889 LEU Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 596 optimal weight: 6.9990 chunk 627 optimal weight: 3.9990 chunk 572 optimal weight: 50.0000 chunk 610 optimal weight: 4.9990 chunk 367 optimal weight: 0.9980 chunk 266 optimal weight: 50.0000 chunk 479 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 551 optimal weight: 0.8980 chunk 577 optimal weight: 6.9990 chunk 608 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 55 GLN ** Q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 ASN s 73 GLN ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 994 ASN ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 57172 Z= 0.464 Angle : 0.661 12.508 78867 Z= 0.337 Chirality : 0.045 0.433 8985 Planarity : 0.005 0.076 9219 Dihedral : 17.180 179.882 11677 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 3.26 % Allowed : 15.22 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.48 (0.11), residues: 6497 helix: 1.59 (0.09), residues: 3199 sheet: -0.27 (0.20), residues: 689 loop : -1.12 (0.13), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1386 HIS 0.010 0.002 HIS r 98 PHE 0.028 0.002 PHE A 898 TYR 0.022 0.002 TYR L 388 ARG 0.007 0.001 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 522 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 429 MET cc_start: 0.8831 (mmm) cc_final: 0.8580 (mmt) REVERT: 7 472 ARG cc_start: 0.7303 (mmt-90) cc_final: 0.7011 (mmt-90) REVERT: C 603 MET cc_start: 0.9110 (ttp) cc_final: 0.8762 (ttp) REVERT: C 641 MET cc_start: 0.8992 (mmm) cc_final: 0.8421 (mmm) REVERT: D 15 ASP cc_start: 0.8253 (m-30) cc_final: 0.8022 (m-30) REVERT: D 88 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8404 (ttpt) REVERT: K 393 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7735 (p90) REVERT: K 402 PHE cc_start: 0.6417 (m-80) cc_final: 0.6136 (m-80) REVERT: M 28 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: Q 5 LYS cc_start: 0.5828 (mttt) cc_final: 0.5326 (tttm) REVERT: Q 76 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: X 24 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6911 (ptm-80) REVERT: r 66 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8629 (mp) REVERT: L 156 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: L 184 LEU cc_start: 0.8048 (tp) cc_final: 0.7602 (mp) REVERT: L 232 MET cc_start: 0.8355 (ptp) cc_final: 0.8006 (mtm) REVERT: L 424 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8549 (tp) REVERT: N 191 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7877 (pp) REVERT: N 339 CYS cc_start: 0.7591 (t) cc_final: 0.6812 (p) REVERT: A 834 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7674 (p90) REVERT: A 984 MET cc_start: 0.8069 (ttm) cc_final: 0.7822 (ttm) REVERT: A 1239 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8140 (ttp-110) REVERT: A 1965 HIS cc_start: 0.7706 (t70) cc_final: 0.7036 (t70) REVERT: S 148 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.1979 (mt-10) REVERT: S 215 ASP cc_start: 0.6504 (m-30) cc_final: 0.6051 (t0) REVERT: S 264 ASP cc_start: 0.7825 (p0) cc_final: 0.7580 (p0) REVERT: T 895 LYS cc_start: 0.8512 (mmmt) cc_final: 0.7925 (mttt) REVERT: J 492 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7238 (p0) outliers start: 154 outliers final: 116 residues processed: 643 average time/residue: 0.5588 time to fit residues: 605.0231 Evaluate side-chains 629 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 501 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 474 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 403 ASP Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 56 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 10 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 144 ASP Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 254 ARG Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1172 ASN Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1509 PHE Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1520 ASN Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1788 VAL Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1874 VAL Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1889 LEU Chi-restraints excluded: chain A residue 1896 CYS Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 148 GLU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 536 ASP Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 401 optimal weight: 0.7980 chunk 645 optimal weight: 30.0000 chunk 394 optimal weight: 0.3980 chunk 306 optimal weight: 10.0000 chunk 448 optimal weight: 0.9990 chunk 677 optimal weight: 3.9990 chunk 623 optimal weight: 50.0000 chunk 539 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 416 optimal weight: 0.6980 chunk 330 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN M 34 GLN Q 55 GLN Q 107 GLN X 35 ASN s 73 GLN ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 HIS ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2043 GLN S 163 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 57172 Z= 0.161 Angle : 0.539 11.849 78867 Z= 0.275 Chirality : 0.039 0.377 8985 Planarity : 0.004 0.063 9219 Dihedral : 17.139 179.870 11677 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 2.01 % Allowed : 16.53 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.76 (0.11), residues: 6497 helix: 1.87 (0.09), residues: 3207 sheet: -0.26 (0.20), residues: 681 loop : -1.03 (0.13), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 750 HIS 0.008 0.001 HIS N 368 PHE 0.014 0.001 PHE A1311 TYR 0.022 0.001 TYR A1991 ARG 0.009 0.000 ARG J 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 532 time to evaluate : 6.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 429 MET cc_start: 0.8630 (mmm) cc_final: 0.8369 (mmt) REVERT: 7 444 ARG cc_start: 0.6513 (ttp80) cc_final: 0.6148 (tmm160) REVERT: 7 472 ARG cc_start: 0.7281 (mmt-90) cc_final: 0.6959 (mmt-90) REVERT: C 603 MET cc_start: 0.8955 (ttp) cc_final: 0.8595 (ttp) REVERT: C 641 MET cc_start: 0.8925 (mmm) cc_final: 0.8308 (mmm) REVERT: D 15 ASP cc_start: 0.8144 (m-30) cc_final: 0.7875 (m-30) REVERT: I 11 SER cc_start: 0.8577 (t) cc_final: 0.8244 (p) REVERT: K 393 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7297 (p90) REVERT: M 28 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: Q 5 LYS cc_start: 0.5612 (mttt) cc_final: 0.5107 (tttp) REVERT: Q 76 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: X 24 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6918 (ptm-80) REVERT: r 66 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8523 (mp) REVERT: L 156 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: L 184 LEU cc_start: 0.8080 (tp) cc_final: 0.7589 (mp) REVERT: L 232 MET cc_start: 0.8382 (ptp) cc_final: 0.7933 (mtm) REVERT: L 424 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8536 (tp) REVERT: N 339 CYS cc_start: 0.7571 (t) cc_final: 0.6979 (p) REVERT: N 382 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6350 (pp) REVERT: A 214 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7817 (ttp80) REVERT: A 984 MET cc_start: 0.8039 (ttm) cc_final: 0.7821 (ttm) REVERT: A 1239 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8064 (ttp-110) REVERT: A 1965 HIS cc_start: 0.7683 (t70) cc_final: 0.7040 (t70) REVERT: S 215 ASP cc_start: 0.6567 (m-30) cc_final: 0.6070 (t0) REVERT: S 264 ASP cc_start: 0.7728 (p0) cc_final: 0.7404 (p0) REVERT: T 862 GLN cc_start: 0.7033 (mm110) cc_final: 0.6309 (tp-100) REVERT: T 881 SER cc_start: 0.8631 (m) cc_final: 0.8093 (p) REVERT: T 895 LYS cc_start: 0.8511 (mmmt) cc_final: 0.7933 (mttt) REVERT: J 492 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7261 (p0) outliers start: 95 outliers final: 72 residues processed: 605 average time/residue: 0.5534 time to fit residues: 560.7486 Evaluate side-chains 602 residues out of total 5831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 521 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain D residue 3 TYR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 78 CYS Chi-restraints excluded: chain Q residue 107 GLN Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 79 ASP Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 73 GLN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 254 ARG Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 377 ILE Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1770 GLU Chi-restraints excluded: chain A residue 1852 LEU Chi-restraints excluded: chain A residue 1929 SER Chi-restraints excluded: chain A residue 1930 TYR Chi-restraints excluded: chain A residue 1947 ASN Chi-restraints excluded: chain A residue 1967 ILE Chi-restraints excluded: chain A residue 2046 THR Chi-restraints excluded: chain A residue 2056 THR Chi-restraints excluded: chain S residue 252 ARG Chi-restraints excluded: chain S residue 272 MET Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain J residue 492 ASP Chi-restraints excluded: chain J residue 546 TYR Chi-restraints excluded: chain J residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 428 optimal weight: 0.5980 chunk 574 optimal weight: 50.0000 chunk 165 optimal weight: 8.9990 chunk 497 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 540 optimal weight: 4.9990 chunk 226 optimal weight: 0.3980 chunk 554 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Q 55 GLN ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN s 73 GLN ** F 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 GLN ** A1615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.139159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106742 restraints weight = 110166.395| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.36 r_work: 0.3254 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 57172 Z= 0.191 Angle : 0.608 59.178 78867 Z= 0.326 Chirality : 0.039 0.452 8985 Planarity : 0.004 0.061 9219 Dihedral : 17.136 179.873 11677 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 1.95 % Allowed : 16.66 % Favored : 81.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.77 (0.11), residues: 6497 helix: 1.87 (0.09), residues: 3207 sheet: -0.25 (0.20), residues: 681 loop : -1.02 (0.13), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 750 HIS 0.006 0.001 HIS A1791 PHE 0.028 0.001 PHE A 169 TYR 0.017 0.001 TYR A1620 ARG 0.007 0.000 ARG J 483 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12976.16 seconds wall clock time: 230 minutes 10.99 seconds (13810.99 seconds total)