Starting phenix.real_space_refine on Thu Sep 26 11:19:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/09_2024/8rdu_19075.cif" } resolution = 2.3 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 ------------------------------------------------------------------------------- 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= -0.006 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 564 5.49 5 Mg 17 5.21 5 S 186 5.16 5 C 36200 2.51 5 N 10992 2.21 5 O 13469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61430 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 5239 Classifications: {'RNA': 246} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 107, 'rna3p_pyr': 101} Link IDs: {'rna2p': 38, 'rna3p': 207} Chain: "2" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1370 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain: "3" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1995 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain: "4" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "5" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "6" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 986 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "7" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4872 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 2 Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "C" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1306 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 150} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "N" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "P" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "Q" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "R" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4043 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 19, 'TRANS': 484} Chain breaks: 1 Chain: "S" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4010 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 19, 'TRANS': 480} Chain breaks: 1 Chain: "T" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2393 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "U" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2419 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 3 Chain: "r" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "s" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "t" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "u" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "2" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "3" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17579 SG CYS C 133 56.961 123.503 245.567 1.00 30.64 S ATOM 17600 SG CYS C 136 54.867 120.539 244.487 1.00 34.07 S ATOM 17716 SG CYS C 151 58.235 120.970 242.975 1.00 40.26 S ATOM 17743 SG CYS C 154 55.485 123.467 242.128 1.00 46.87 S ATOM 17304 SG CYS C 100 67.729 131.559 251.672 1.00 34.05 S ATOM 17319 SG CYS C 103 71.291 131.768 250.577 1.00 29.68 S ATOM 17488 SG CYS C 122 70.335 133.064 254.035 1.00 35.65 S Time building chain proxies: 29.69, per 1000 atoms: 0.48 Number of scatterers: 61430 At special positions: 0 Unit cell: (147.056, 152.88, 329.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 186 16.00 P 564 15.00 Mg 17 11.99 O 13469 8.00 N 10992 7.00 C 36200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.93 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 200 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 136 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 151 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 133 " pdb="ZN ZN C 200 " - pdb=" SG CYS C 154 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 125 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 122 " Number of angles added : 9 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11448 Finding SS restraints... Secondary structure from input PDB file: 303 helices and 33 sheets defined 58.2% alpha, 9.6% beta 197 base pairs and 363 stacking pairs defined. Time for finding SS restraints: 19.53 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 Processing helix chain 'A' and resid 27 through 40 Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.532A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 76 through 115 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.729A pdb=" N GLU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.641A pdb=" N GLN A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.532A pdb=" N ASN A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 232 Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.167A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.582A pdb=" N LYS A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 508 removed outlier: 4.086A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.600A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 578 through 588 Processing helix chain 'A' and resid 589 through 604 Processing helix chain 'A' and resid 618 through 633 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 25 through 47 removed outlier: 3.566A pdb=" N ALA B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 73 removed outlier: 3.641A pdb=" N GLY B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.567A pdb=" N ARG C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.840A pdb=" N VAL C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.544A pdb=" N ALA C 162 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 165 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 52 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 151 No H-bonds generated for 'chain 'D' and resid 150 through 151' Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.678A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.777A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.710A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.572A pdb=" N ARG E 74 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.860A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 30 removed outlier: 3.839A pdb=" N GLY F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.513A pdb=" N ARG F 74 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 146 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.813A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 146 through 149 Processing helix chain 'G' and resid 152 through 164 removed outlier: 4.173A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.944A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.634A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 146 through 149 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 173 through 182 removed outlier: 3.903A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 Processing helix chain 'H' and resid 240 through 258 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 30 removed outlier: 3.785A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.675A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 30 removed outlier: 3.847A pdb=" N GLY J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 151 No H-bonds generated for 'chain 'J' and resid 150 through 151' Processing helix chain 'J' and resid 152 through 164 removed outlier: 4.300A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 182 removed outlier: 3.714A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS J 181 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.594A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 101 through 113 Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.089A pdb=" N ASP K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 182 removed outlier: 3.878A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'L' and resid 20 through 29 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 134 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 173 through 181 removed outlier: 3.780A pdb=" N ASP L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.543A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 3.894A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'M' and resid 20 through 29 Processing helix chain 'M' and resid 36 through 53 Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 101 through 113 Processing helix chain 'M' and resid 121 through 134 Processing helix chain 'M' and resid 146 through 149 Processing helix chain 'M' and resid 150 through 151 No H-bonds generated for 'chain 'M' and resid 150 through 151' Processing helix chain 'M' and resid 152 through 164 removed outlier: 4.266A pdb=" N ASP M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.994A pdb=" N ASP M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 200 through 215 Processing helix chain 'M' and resid 226 through 238 removed outlier: 4.002A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 258 Processing helix chain 'M' and resid 264 through 274 removed outlier: 3.877A pdb=" N GLU M 274 " --> pdb=" O GLU M 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 36 through 53 Processing helix chain 'N' and resid 65 through 77 Processing helix chain 'N' and resid 101 through 113 Processing helix chain 'N' and resid 121 through 134 Processing helix chain 'N' and resid 146 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 153 through 164 Processing helix chain 'N' and resid 173 through 181 removed outlier: 3.832A pdb=" N ASP N 177 " --> pdb=" O THR N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 190 Processing helix chain 'N' and resid 200 through 215 removed outlier: 3.853A pdb=" N GLU N 212 " --> pdb=" O VAL N 208 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN N 213 " --> pdb=" O GLU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 238 removed outlier: 4.087A pdb=" N ILE N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 258 Processing helix chain 'N' and resid 264 through 273 Processing helix chain 'O' and resid 20 through 30 Processing helix chain 'O' and resid 36 through 53 Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 121 through 134 Processing helix chain 'O' and resid 146 through 149 Processing helix chain 'O' and resid 152 through 164 removed outlier: 4.125A pdb=" N ASP O 156 " --> pdb=" O GLU O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.838A pdb=" N ASP O 177 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 190 Processing helix chain 'O' and resid 201 through 215 Processing helix chain 'O' and resid 226 through 238 Processing helix chain 'O' and resid 240 through 258 removed outlier: 3.694A pdb=" N GLU O 246 " --> pdb=" O GLY O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 273 removed outlier: 3.992A pdb=" N GLU O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 Processing helix chain 'P' and resid 36 through 53 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'P' and resid 121 through 134 Processing helix chain 'P' and resid 145 through 149 Processing helix chain 'P' and resid 153 through 164 Processing helix chain 'P' and resid 173 through 182 removed outlier: 3.834A pdb=" N ASP P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 200 through 214 Processing helix chain 'P' and resid 228 through 238 removed outlier: 3.955A pdb=" N ILE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 259 removed outlier: 4.483A pdb=" N GLU P 246 " --> pdb=" O GLY P 242 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 273 removed outlier: 3.645A pdb=" N GLU P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 30 removed outlier: 4.025A pdb=" N ARG Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 53 Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 101 through 113 Processing helix chain 'Q' and resid 121 through 134 Processing helix chain 'Q' and resid 146 through 149 Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.890A pdb=" N ASP Q 156 " --> pdb=" O GLU Q 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 182 removed outlier: 3.873A pdb=" N ASP Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 190 Processing helix chain 'Q' and resid 200 through 215 removed outlier: 3.954A pdb=" N GLU Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 238 removed outlier: 3.648A pdb=" N ALA Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 257 removed outlier: 4.305A pdb=" N GLU Q 246 " --> pdb=" O GLY Q 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 273 Processing helix chain 'R' and resid 39 through 53 Processing helix chain 'R' and resid 57 through 73 removed outlier: 3.775A pdb=" N GLY R 62 " --> pdb=" O ARG R 58 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS R 71 " --> pdb=" O GLU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 90 removed outlier: 3.662A pdb=" N VAL R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 95 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 130 through 146 Processing helix chain 'R' and resid 152 through 170 Proline residue: R 162 - end of helix removed outlier: 3.705A pdb=" N ALA R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 294 through 305 Processing helix chain 'R' and resid 313 through 316 Processing helix chain 'R' and resid 317 through 331 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 332 through 335 Processing helix chain 'R' and resid 349 through 354 Processing helix chain 'R' and resid 357 through 372 removed outlier: 3.589A pdb=" N ARG R 367 " --> pdb=" O GLN R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 376 Processing helix chain 'R' and resid 387 through 392 Processing helix chain 'R' and resid 402 through 411 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.622A pdb=" N CYS R 423 " --> pdb=" O ARG R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 440 removed outlier: 3.540A pdb=" N GLY R 438 " --> pdb=" O TYR R 435 " (cutoff:3.500A) Processing helix chain 'R' and resid 483 through 495 removed outlier: 3.506A pdb=" N SER R 491 " --> pdb=" O ALA R 487 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG R 495 " --> pdb=" O SER R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 496 through 498 No H-bonds generated for 'chain 'R' and resid 496 through 498' Processing helix chain 'R' and resid 502 through 509 Processing helix chain 'R' and resid 525 through 539 removed outlier: 4.164A pdb=" N ALA R 538 " --> pdb=" O LEU R 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL R 539 " --> pdb=" O ARG R 535 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 54 removed outlier: 3.676A pdb=" N GLU S 54 " --> pdb=" O GLN S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 65 removed outlier: 3.948A pdb=" N GLN S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 73 removed outlier: 3.538A pdb=" N LYS S 71 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 95 removed outlier: 8.748A pdb=" N LEU S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL S 92 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY S 93 " --> pdb=" O ASP S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 123 removed outlier: 4.512A pdb=" N TRP S 111 " --> pdb=" O ILE S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 146 Processing helix chain 'S' and resid 152 through 170 Proline residue: S 162 - end of helix Processing helix chain 'S' and resid 248 through 261 removed outlier: 3.721A pdb=" N LEU S 261 " --> pdb=" O ARG S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 305 Processing helix chain 'S' and resid 313 through 316 Processing helix chain 'S' and resid 317 through 331 Proline residue: S 323 - end of helix Processing helix chain 'S' and resid 332 through 335 Processing helix chain 'S' and resid 342 through 346 Processing helix chain 'S' and resid 349 through 354 Processing helix chain 'S' and resid 357 through 372 removed outlier: 4.081A pdb=" N GLN S 363 " --> pdb=" O ARG S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 392 removed outlier: 3.531A pdb=" N TRP S 390 " --> pdb=" O ARG S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 402 through 407 removed outlier: 3.822A pdb=" N LEU S 406 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 439 Processing helix chain 'S' and resid 461 through 465 Processing helix chain 'S' and resid 483 through 497 removed outlier: 3.699A pdb=" N ARG S 492 " --> pdb=" O GLU S 488 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 493 " --> pdb=" O ALA S 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA S 497 " --> pdb=" O ARG S 493 " (cutoff:3.500A) Processing helix chain 'S' and resid 502 through 512 removed outlier: 3.606A pdb=" N GLN S 508 " --> pdb=" O GLN S 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL S 511 " --> pdb=" O LEU S 507 " (cutoff:3.500A) Processing helix chain 'S' and resid 526 through 535 Processing helix chain 'S' and resid 537 through 541 Processing helix chain 'T' and resid 248 through 261 removed outlier: 3.987A pdb=" N VAL T 252 " --> pdb=" O SER T 248 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG T 257 " --> pdb=" O ALA T 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU T 261 " --> pdb=" O ARG T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 Processing helix chain 'T' and resid 295 through 305 removed outlier: 3.923A pdb=" N GLN T 299 " --> pdb=" O ASN T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 330 removed outlier: 3.536A pdb=" N ASN T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 331 through 335 removed outlier: 3.678A pdb=" N LEU T 335 " --> pdb=" O PHE T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 357 through 371 removed outlier: 3.592A pdb=" N VAL T 366 " --> pdb=" O GLU T 362 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG T 367 " --> pdb=" O GLN T 363 " (cutoff:3.500A) Processing helix chain 'T' and resid 385 through 394 Processing helix chain 'T' and resid 403 through 407 removed outlier: 3.788A pdb=" N ASP T 407 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 440 removed outlier: 3.560A pdb=" N ALA T 440 " --> pdb=" O ALA T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 483 through 501 removed outlier: 3.551A pdb=" N THR T 500 " --> pdb=" O THR T 496 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE T 501 " --> pdb=" O ALA T 497 " (cutoff:3.500A) Processing helix chain 'T' and resid 503 through 518 removed outlier: 4.496A pdb=" N VAL T 510 " --> pdb=" O LEU T 506 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL T 511 " --> pdb=" O LEU T 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 261 Processing helix chain 'U' and resid 296 through 305 removed outlier: 3.652A pdb=" N ILE U 300 " --> pdb=" O HIS U 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY U 301 " --> pdb=" O LEU U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 323 through 327 Processing helix chain 'U' and resid 331 through 335 Processing helix chain 'U' and resid 359 through 367 removed outlier: 4.466A pdb=" N GLN U 363 " --> pdb=" O ARG U 359 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU U 365 " --> pdb=" O LEU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 372 Processing helix chain 'U' and resid 378 through 382 removed outlier: 3.648A pdb=" N GLY U 382 " --> pdb=" O ALA U 379 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 393 removed outlier: 3.689A pdb=" N TRP U 390 " --> pdb=" O ARG U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 402 through 410 removed outlier: 3.700A pdb=" N LEU U 406 " --> pdb=" O GLU U 403 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP U 407 " --> pdb=" O ARG U 404 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE U 408 " --> pdb=" O ASP U 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS U 409 " --> pdb=" O LEU U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 423 Processing helix chain 'U' and resid 435 through 440 removed outlier: 3.509A pdb=" N GLY U 438 " --> pdb=" O TYR U 435 " (cutoff:3.500A) Processing helix chain 'U' and resid 483 through 499 removed outlier: 3.539A pdb=" N LEU U 494 " --> pdb=" O ALA U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 500 through 501 No H-bonds generated for 'chain 'U' and resid 500 through 501' Processing helix chain 'U' and resid 502 through 506 removed outlier: 3.573A pdb=" N SER U 505 " --> pdb=" O SER U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 507 through 520 removed outlier: 3.558A pdb=" N VAL U 511 " --> pdb=" O LEU U 507 " (cutoff:3.500A) Processing helix chain 'r' and resid 575 through 583 removed outlier: 3.617A pdb=" N ARG r 579 " --> pdb=" O TYR r 575 " (cutoff:3.500A) Processing helix chain 's' and resid 574 through 583 Processing helix chain 't' and resid 575 through 583 removed outlier: 3.899A pdb=" N GLY t 583 " --> pdb=" O ARG t 579 " (cutoff:3.500A) Processing helix chain 'u' and resid 575 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.562A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 475 removed outlier: 6.558A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY A 541 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU A 609 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 543 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY A 611 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 545 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.542A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP F 144 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE F 94 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.550A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP G 144 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE G 94 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.550A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 94 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.500A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP I 144 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE I 94 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.529A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.504A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP K 144 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE K 94 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.615A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 33 removed outlier: 3.806A pdb=" N TRP r 573 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 91 through 94 removed outlier: 6.521A pdb=" N VAL M 92 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP M 144 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE M 94 " --> pdb=" O ASP M 144 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU M 141 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL M 171 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE M 143 " --> pdb=" O VAL M 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'N' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL N 92 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP N 144 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE N 94 " --> pdb=" O ASP N 144 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU N 141 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL N 171 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE N 143 " --> pdb=" O VAL N 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 91 through 94 removed outlier: 6.511A pdb=" N VAL O 92 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP O 144 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE O 94 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'P' and resid 91 through 94 removed outlier: 6.549A pdb=" N VAL P 92 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG P 57 " --> pdb=" O LEU P 194 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE P 196 " --> pdb=" O ARG P 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL P 59 " --> pdb=" O PHE P 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'R' and resid 33 through 35 removed outlier: 5.782A pdb=" N PHE T 468 " --> pdb=" O ARG T 460 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG T 460 " --> pdb=" O PHE T 468 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN T 461 " --> pdb=" O THR T 443 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N THR T 443 " --> pdb=" O GLN T 461 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU T 446 " --> pdb=" O SER T 414 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER T 414 " --> pdb=" O LEU T 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 33 through 35 removed outlier: 4.693A pdb=" N MET T 430 " --> pdb=" O GLN T 475 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 184 through 186 Processing sheet with id=AC6, first strand: chain 'R' and resid 237 through 243 removed outlier: 6.003A pdb=" N ILE R 237 " --> pdb=" O ASP R 231 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP R 231 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP R 202 " --> pdb=" O TYR R 285 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 284 " --> pdb=" O HIS R 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 213 through 214 Processing sheet with id=AC8, first strand: chain 'R' and resid 412 through 417 removed outlier: 8.432A pdb=" N THR R 443 " --> pdb=" O GLN R 461 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN R 461 " --> pdb=" O THR R 443 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP R 449 " --> pdb=" O THR R 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR R 455 " --> pdb=" O ASP R 449 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR R 454 " --> pdb=" O HIS R 473 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS R 473 " --> pdb=" O THR R 454 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE R 456 " --> pdb=" O ARG R 471 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG R 471 " --> pdb=" O ILE R 456 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL R 458 " --> pdb=" O LEU R 469 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU R 429 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 424 " --> pdb=" O TYR R 431 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 33 through 35 removed outlier: 5.548A pdb=" N PHE U 468 " --> pdb=" O ARG U 460 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG U 460 " --> pdb=" O PHE U 468 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN U 461 " --> pdb=" O THR U 443 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR U 443 " --> pdb=" O GLN U 461 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU U 446 " --> pdb=" O SER U 414 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER U 414 " --> pdb=" O LEU U 446 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 33 through 35 Processing sheet with id=AD2, first strand: chain 'S' and resid 184 through 186 Processing sheet with id=AD3, first strand: chain 'S' and resid 236 through 243 removed outlier: 6.085A pdb=" N ILE S 237 " --> pdb=" O ASP S 231 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP S 231 " --> pdb=" O ILE S 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY S 239 " --> pdb=" O VAL S 229 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP S 205 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TRP S 202 " --> pdb=" O TYR S 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 411 through 418 removed outlier: 5.661A pdb=" N LYS S 412 " --> pdb=" O PHE S 448 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE S 448 " --> pdb=" O LYS S 412 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER S 414 " --> pdb=" O LEU S 446 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU S 446 " --> pdb=" O SER S 414 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG S 416 " --> pdb=" O VAL S 444 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP S 449 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR S 455 " --> pdb=" O ASP S 449 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR S 454 " --> pdb=" O HIS S 473 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS S 473 " --> pdb=" O THR S 454 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE S 456 " --> pdb=" O ARG S 471 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG S 471 " --> pdb=" O ILE S 456 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL S 458 " --> pdb=" O LEU S 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 237 through 243 removed outlier: 7.023A pdb=" N ILE T 237 " --> pdb=" O ASP T 231 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP T 231 " --> pdb=" O ILE T 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 237 through 243 removed outlier: 6.601A pdb=" N ILE U 237 " --> pdb=" O ASP U 231 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP U 231 " --> pdb=" O ILE U 237 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY U 239 " --> pdb=" O VAL U 229 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TRP U 202 " --> pdb=" O TYR U 285 " (cutoff:3.500A) 2545 hydrogen bonds defined for protein. 7344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 488 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 363 stacking parallelities Total time for adding SS restraints: 29.90 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9704 1.32 - 1.44: 18193 1.44 - 1.57: 33422 1.57 - 1.69: 1099 1.69 - 1.81: 274 Bond restraints: 62692 Sorted by residual: bond pdb=" N ILE C 97 " pdb=" CA ILE C 97 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.20e-02 6.94e+03 1.22e+01 bond pdb=" CE1 HIS C 94 " pdb=" NE2 HIS C 94 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.20e+01 bond pdb=" N GLN C 93 " pdb=" CA GLN C 93 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.57e+00 bond pdb=" N ASP L 144 " pdb=" CA ASP L 144 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.26e+00 bond pdb=" N ASP I 144 " pdb=" CA ASP I 144 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.30e-02 5.92e+03 5.24e+00 ... (remaining 62687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 84194 2.25 - 4.49: 2571 4.49 - 6.74: 207 6.74 - 8.99: 13 8.99 - 11.23: 1 Bond angle restraints: 86986 Sorted by residual: angle pdb=" C3' DT 3 130 " pdb=" O3' DT 3 130 " pdb=" P DC 3 131 " ideal model delta sigma weight residual 120.20 108.97 11.23 1.50e+00 4.44e-01 5.61e+01 angle pdb=" O3' A 1 196 " pdb=" C3' A 1 196 " pdb=" C2' A 1 196 " ideal model delta sigma weight residual 109.50 118.09 -8.59 1.50e+00 4.44e-01 3.28e+01 angle pdb=" C4' DA 6 57 " pdb=" C3' DA 6 57 " pdb=" O3' DA 6 57 " ideal model delta sigma weight residual 110.00 117.92 -7.92 1.50e+00 4.44e-01 2.79e+01 angle pdb=" C3' DT 3 129 " pdb=" O3' DT 3 129 " pdb=" P DT 3 130 " ideal model delta sigma weight residual 120.20 112.68 7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" C2' DA 6 74 " pdb=" C1' DA 6 74 " pdb=" N9 DA 6 74 " ideal model delta sigma weight residual 113.50 120.55 -7.05 1.50e+00 4.44e-01 2.21e+01 ... (remaining 86981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 35913 35.98 - 71.95: 2231 71.95 - 107.92: 125 107.92 - 143.90: 8 143.90 - 179.87: 18 Dihedral angle restraints: 38295 sinusoidal: 20592 harmonic: 17703 Sorted by residual: dihedral pdb=" O4' U 1 170 " pdb=" C1' U 1 170 " pdb=" N1 U 1 170 " pdb=" C2 U 1 170 " ideal model delta sinusoidal sigma weight residual 200.00 33.03 166.97 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U 1 41 " pdb=" C1' U 1 41 " pdb=" N1 U 1 41 " pdb=" C2 U 1 41 " ideal model delta sinusoidal sigma weight residual 200.00 36.48 163.52 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U 1 39 " pdb=" C1' U 1 39 " pdb=" N1 U 1 39 " pdb=" C2 U 1 39 " ideal model delta sinusoidal sigma weight residual 200.00 38.23 161.77 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 38292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 9482 0.124 - 0.247: 379 0.247 - 0.371: 31 0.371 - 0.494: 7 0.494 - 0.618: 1 Chirality restraints: 9900 Sorted by residual: chirality pdb=" C3' A 1 196 " pdb=" C4' A 1 196 " pdb=" O3' A 1 196 " pdb=" C2' A 1 196 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.62 2.00e-01 2.50e+01 9.54e+00 chirality pdb=" C3' DA 2 5 " pdb=" C4' DA 2 5 " pdb=" O3' DA 2 5 " pdb=" C2' DA 2 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P DT 3 129 " pdb=" OP1 DT 3 129 " pdb=" OP2 DT 3 129 " pdb=" O5' DT 3 129 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 9897 not shown) Planarity restraints: 9171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 1 99 " 0.084 2.00e-02 2.50e+03 4.90e-02 5.40e+01 pdb=" N1 C 1 99 " -0.075 2.00e-02 2.50e+03 pdb=" C2 C 1 99 " -0.024 2.00e-02 2.50e+03 pdb=" O2 C 1 99 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C 1 99 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C 1 99 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 1 99 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C 1 99 " 0.059 2.00e-02 2.50e+03 pdb=" C6 C 1 99 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 127 " -0.079 2.00e-02 2.50e+03 4.74e-02 5.05e+01 pdb=" N1 U 1 127 " 0.074 2.00e-02 2.50e+03 pdb=" C2 U 1 127 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 1 127 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U 1 127 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U 1 127 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U 1 127 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U 1 127 " -0.057 2.00e-02 2.50e+03 pdb=" C6 U 1 127 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 1 245 " 0.063 2.00e-02 2.50e+03 3.96e-02 3.52e+01 pdb=" N1 C 1 245 " -0.051 2.00e-02 2.50e+03 pdb=" C2 C 1 245 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C 1 245 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C 1 245 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C 1 245 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C 1 245 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 1 245 " 0.053 2.00e-02 2.50e+03 pdb=" C6 C 1 245 " -0.068 2.00e-02 2.50e+03 ... (remaining 9168 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 186 2.37 - 3.00: 32316 3.00 - 3.64: 98437 3.64 - 4.27: 159697 4.27 - 4.90: 245496 Nonbonded interactions: 536132 Sorted by model distance: nonbonded pdb=" O2B ATP O 300 " pdb="MG MG O 301 " model vdw 1.739 2.170 nonbonded pdb=" O2B ATP D 300 " pdb="MG MG D 301 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR E 67 " pdb="MG MG E 301 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR D 67 " pdb="MG MG D 301 " model vdw 1.999 2.170 nonbonded pdb=" OG1 THR F 67 " pdb="MG MG F 301 " model vdw 2.011 2.170 ... (remaining 536127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '4' and (resid 16 through 26 or resid 28 through 33 or resid 35 through 4 \ 0)) selection = (chain '5' and ((resid 16 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or \ name N3 or name C4 or name O4 or name C5 or name C7 or name C6 )) or resid 17 th \ rough 26 or resid 28 through 33 or resid 35 through 40)) } ncs_group { reference = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) selection = (chain 'K' and resid 19 through 275) selection = (chain 'L' and resid 19 through 275) selection = (chain 'M' and resid 19 through 275) selection = (chain 'N' and resid 19 through 275) selection = (chain 'O' and resid 19 through 275) selection = (chain 'P' and resid 19 through 275) selection = (chain 'Q' and resid 19 through 275) } ncs_group { reference = (chain 'R' and (resid 31 through 512 or resid 525 through 542 or resid 600)) selection = chain 'S' } ncs_group { reference = (chain 'T' and (resid 196 through 287 or resid 295 through 339 or resid 354 thro \ ugh 522)) selection = (chain 'U' and (resid 196 through 311 or resid 323 through 522)) } ncs_group { reference = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.330 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 140.960 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.470 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.006 0.075 62692 Z= 0.358 Angle : 0.886 11.232 86986 Z= 0.535 Chirality : 0.062 0.618 9900 Planarity : 0.012 0.176 9171 Dihedral : 19.920 179.875 26847 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.77 % Allowed : 5.82 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 6033 helix: -1.00 (0.08), residues: 3249 sheet: -0.07 (0.21), residues: 480 loop : -0.20 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP M 45 HIS 0.015 0.002 HIS A 353 PHE 0.029 0.003 PHE R 284 TYR 0.030 0.005 TYR R 233 ARG 0.034 0.004 ARG S 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 939 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 GLN cc_start: 0.7952 (tp40) cc_final: 0.7682 (tp-100) REVERT: A 492 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.7564 (ttp80) REVERT: A 539 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8510 (mppt) REVERT: A 612 LYS cc_start: 0.7841 (tppt) cc_final: 0.7592 (mptp) REVERT: B 9 LYS cc_start: 0.7287 (ttpt) cc_final: 0.6409 (ttpt) REVERT: C 84 MET cc_start: 0.8931 (mtp) cc_final: 0.8728 (mtp) REVERT: D 107 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7559 (ttpp) REVERT: D 227 LYS cc_start: 0.6491 (mttp) cc_final: 0.6160 (mptm) REVERT: E 140 MET cc_start: 0.9161 (ttm) cc_final: 0.8851 (ttm) REVERT: E 225 LYS cc_start: 0.7490 (tptp) cc_final: 0.7067 (pptt) REVERT: E 231 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7542 (tpp-160) REVERT: E 270 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7403 (mt-10) REVERT: F 131 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7668 (mm-30) REVERT: F 209 GLU cc_start: 0.8250 (tt0) cc_final: 0.8034 (tt0) REVERT: F 210 MET cc_start: 0.8476 (mtp) cc_final: 0.8067 (mtp) REVERT: G 225 LYS cc_start: 0.7424 (pmmt) cc_final: 0.7205 (ptpp) REVERT: G 269 GLN cc_start: 0.7424 (mm110) cc_final: 0.7036 (mt0) REVERT: G 273 LYS cc_start: 0.8332 (ptmm) cc_final: 0.8024 (pttm) REVERT: H 261 LYS cc_start: 0.7979 (mptt) cc_final: 0.7510 (mmtm) REVERT: I 78 LYS cc_start: 0.7124 (pmmt) cc_final: 0.6820 (pmtt) REVERT: J 38 GLN cc_start: 0.8425 (tt0) cc_final: 0.8201 (tt0) REVERT: J 196 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8210 (t80) REVERT: J 229 MET cc_start: 0.7694 (mmm) cc_final: 0.7410 (mmm) REVERT: K 22 GLN cc_start: 0.7829 (mp10) cc_final: 0.7416 (mm-40) REVERT: K 175 ARG cc_start: 0.8474 (ttm170) cc_final: 0.8189 (ttp80) REVERT: L 103 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8483 (ttpp) REVERT: L 116 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8275 (mmm-85) REVERT: L 231 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6974 (tpp-160) REVERT: M 82 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6657 (tt0) REVERT: M 184 GLU cc_start: 0.7930 (tt0) cc_final: 0.7378 (pt0) REVERT: M 205 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7465 (mttt) REVERT: N 27 ARG cc_start: 0.6161 (ttp80) cc_final: 0.5843 (ttp-170) REVERT: N 37 GLN cc_start: 0.7549 (tp40) cc_final: 0.7347 (tp40) REVERT: N 246 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6475 (tp30) REVERT: O 229 MET cc_start: 0.6252 (mmm) cc_final: 0.5896 (mmm) REVERT: O 238 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: O 269 GLN cc_start: 0.7564 (tp40) cc_final: 0.7307 (tp-100) REVERT: Q 63 ARG cc_start: 0.6266 (mmt90) cc_final: 0.5604 (mmp-170) REVERT: Q 214 MET cc_start: 0.4832 (mpt) cc_final: 0.4363 (mpp) REVERT: Q 229 MET cc_start: 0.3164 (mpt) cc_final: 0.1889 (tpp) REVERT: R 67 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.5522 (pp20) REVERT: R 112 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8068 (mt-10) REVERT: R 165 GLU cc_start: 0.8580 (tp30) cc_final: 0.8230 (tp30) REVERT: R 172 SER cc_start: 0.7528 (t) cc_final: 0.7148 (p) REVERT: R 188 ARG cc_start: 0.7493 (ttm170) cc_final: 0.6804 (tmm160) REVERT: R 215 ASP cc_start: 0.7008 (t0) cc_final: 0.6799 (t0) REVERT: R 345 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7481 (mm-30) REVERT: R 362 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: R 451 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8406 (mtm-85) REVERT: S 375 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: S 378 ASP cc_start: 0.8067 (t0) cc_final: 0.7126 (m-30) REVERT: S 430 MET cc_start: 0.8136 (mtp) cc_final: 0.7885 (mpp) REVERT: S 503 ASN cc_start: 0.7494 (p0) cc_final: 0.7278 (p0) REVERT: T 202 TRP cc_start: 0.6272 (m100) cc_final: 0.5805 (m-10) REVERT: T 277 THR cc_start: 0.8384 (p) cc_final: 0.8173 (p) REVERT: T 327 LEU cc_start: 0.6328 (mm) cc_final: 0.6044 (mm) REVERT: T 338 TYR cc_start: 0.5984 (p90) cc_final: 0.5782 (p90) REVERT: T 373 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.4174 (t80) REVERT: U 238 MET cc_start: 0.3667 (ptm) cc_final: 0.2678 (pmm) REVERT: U 245 ASP cc_start: 0.7109 (t0) cc_final: 0.6689 (t0) REVERT: t 575 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.3182 (m-80) outliers start: 41 outliers final: 5 residues processed: 970 average time/residue: 1.8276 time to fit residues: 2165.2316 Evaluate side-chains 710 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 696 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 255 SER Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain O residue 238 GLU Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 339 THR Chi-restraints excluded: chain R residue 362 GLU Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 6.9990 chunk 488 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 504 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 306 optimal weight: 20.0000 chunk 375 optimal weight: 6.9990 chunk 584 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 80 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 135 ASN C 137 GLN C 165 GLN G 206 ASN H 38 GLN H 213 GLN K 81 GLN K 206 ASN N 81 GLN Q 81 GLN R 217 HIS ** R 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 531 GLN S 344 GLN S 363 GLN S 445 ASN T 375 GLN T 481 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 62692 Z= 0.282 Angle : 0.679 10.421 86986 Z= 0.371 Chirality : 0.045 0.318 9900 Planarity : 0.005 0.064 9171 Dihedral : 21.964 179.618 14248 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.18 % Allowed : 10.65 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 6033 helix: 0.51 (0.09), residues: 3346 sheet: -0.07 (0.22), residues: 490 loop : 0.31 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP S 86 HIS 0.014 0.001 HIS T 296 PHE 0.022 0.002 PHE S 306 TYR 0.025 0.002 TYR T 459 ARG 0.016 0.001 ARG S 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 720 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: A 275 ARG cc_start: 0.7671 (tmm160) cc_final: 0.6840 (mpt180) REVERT: A 362 LYS cc_start: 0.7703 (mptt) cc_final: 0.7398 (mmtt) REVERT: A 416 GLN cc_start: 0.7807 (tp40) cc_final: 0.7550 (tp-100) REVERT: A 456 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: A 492 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: A 539 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8432 (mppt) REVERT: A 566 LYS cc_start: 0.8033 (tttp) cc_final: 0.7764 (ttmp) REVERT: B 9 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6934 (ttmt) REVERT: B 27 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: D 107 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7511 (ttpp) REVERT: D 229 MET cc_start: 0.7395 (mmt) cc_final: 0.7184 (mmt) REVERT: E 131 GLU cc_start: 0.8033 (tp30) cc_final: 0.7759 (mm-30) REVERT: E 140 MET cc_start: 0.9103 (ttm) cc_final: 0.8875 (ttm) REVERT: E 225 LYS cc_start: 0.7129 (tptp) cc_final: 0.6923 (ttpp) REVERT: E 270 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6949 (mp0) REVERT: F 209 GLU cc_start: 0.8111 (tt0) cc_final: 0.7768 (tp30) REVERT: F 210 MET cc_start: 0.8421 (mtp) cc_final: 0.8211 (mtp) REVERT: F 213 GLN cc_start: 0.7572 (mt0) cc_final: 0.7288 (mt0) REVERT: F 261 LYS cc_start: 0.7520 (mttt) cc_final: 0.7145 (mppt) REVERT: G 225 LYS cc_start: 0.7375 (pmmt) cc_final: 0.7090 (ptpp) REVERT: G 269 GLN cc_start: 0.7424 (mm110) cc_final: 0.7011 (mt0) REVERT: G 273 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8078 (pttp) REVERT: H 209 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: H 261 LYS cc_start: 0.7989 (mptt) cc_final: 0.7395 (mptm) REVERT: I 78 LYS cc_start: 0.7185 (pmmt) cc_final: 0.6838 (pmtt) REVERT: I 114 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7837 (mtpp) REVERT: J 78 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7299 (mmmt) REVERT: J 131 GLU cc_start: 0.8214 (tt0) cc_final: 0.7991 (tm-30) REVERT: J 196 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8219 (t80) REVERT: J 206 ASN cc_start: 0.8212 (m-40) cc_final: 0.7955 (m-40) REVERT: K 22 GLN cc_start: 0.7835 (mp10) cc_final: 0.7409 (mm-40) REVERT: K 149 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8114 (mp) REVERT: K 175 ARG cc_start: 0.8240 (ttm170) cc_final: 0.8001 (ttp80) REVERT: L 225 LYS cc_start: 0.7828 (pptt) cc_final: 0.7410 (ptmm) REVERT: M 175 ARG cc_start: 0.7464 (tpt-90) cc_final: 0.7218 (tpt170) REVERT: M 184 GLU cc_start: 0.7929 (tt0) cc_final: 0.7719 (pm20) REVERT: M 205 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7424 (mttt) REVERT: N 275 TYR cc_start: 0.6837 (m-80) cc_final: 0.6455 (m-80) REVERT: O 71 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: O 269 GLN cc_start: 0.7332 (tp40) cc_final: 0.7007 (tp-100) REVERT: O 273 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7567 (ttmt) REVERT: P 182 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6688 (mtp180) REVERT: P 205 LYS cc_start: 0.6999 (mttp) cc_final: 0.6712 (mtmm) REVERT: P 209 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6074 (tm-30) REVERT: P 249 ARG cc_start: 0.6711 (mtt-85) cc_final: 0.6357 (mpt-90) REVERT: Q 128 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6429 (tpt170) REVERT: Q 214 MET cc_start: 0.4817 (mpt) cc_final: 0.4454 (mpp) REVERT: Q 229 MET cc_start: 0.3087 (mpt) cc_final: 0.1809 (tpp) REVERT: R 165 GLU cc_start: 0.8560 (tp30) cc_final: 0.8249 (tp30) REVERT: R 172 SER cc_start: 0.7257 (t) cc_final: 0.6834 (p) REVERT: R 188 ARG cc_start: 0.7628 (ttm170) cc_final: 0.6780 (tmm160) REVERT: R 345 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7614 (mm-30) REVERT: R 381 MET cc_start: 0.8667 (mmm) cc_final: 0.8305 (mmm) REVERT: R 434 GLU cc_start: 0.8090 (pt0) cc_final: 0.7826 (pt0) REVERT: R 465 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8212 (mm110) REVERT: S 375 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: S 378 ASP cc_start: 0.8204 (t0) cc_final: 0.7348 (m-30) REVERT: T 268 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: T 373 TYR cc_start: 0.5277 (OUTLIER) cc_final: 0.4272 (t80) REVERT: T 461 GLN cc_start: 0.7543 (tp40) cc_final: 0.7297 (mm110) REVERT: U 238 MET cc_start: 0.2795 (ptm) cc_final: 0.2107 (pmm) REVERT: U 245 ASP cc_start: 0.7001 (t0) cc_final: 0.6550 (t0) REVERT: U 324 PHE cc_start: 0.7813 (p90) cc_final: 0.7483 (p90) REVERT: U 434 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: U 473 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5635 (m90) REVERT: s 575 TYR cc_start: 0.3549 (OUTLIER) cc_final: 0.2786 (t80) REVERT: t 575 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3386 (m-80) outliers start: 116 outliers final: 26 residues processed: 784 average time/residue: 1.8146 time to fit residues: 1742.7630 Evaluate side-chains 677 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 633 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain s residue 575 TYR Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 486 optimal weight: 20.0000 chunk 398 optimal weight: 0.0670 chunk 161 optimal weight: 6.9990 chunk 585 optimal weight: 40.0000 chunk 632 optimal weight: 9.9990 chunk 521 optimal weight: 10.0000 chunk 580 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 470 optimal weight: 30.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN B 80 GLN C 33 ASN G 206 ASN J 38 GLN K 81 GLN K 206 ASN N 81 GLN Q 81 GLN R 217 HIS S 123 ASN T 199 ASN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 62692 Z= 0.300 Angle : 0.649 11.817 86986 Z= 0.353 Chirality : 0.044 0.335 9900 Planarity : 0.005 0.112 9171 Dihedral : 21.932 178.124 14226 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.57 % Allowed : 12.51 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 6033 helix: 0.84 (0.09), residues: 3340 sheet: -0.29 (0.21), residues: 498 loop : 0.29 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 225 HIS 0.011 0.001 HIS L 77 PHE 0.025 0.002 PHE S 306 TYR 0.023 0.002 TYR R 233 ARG 0.010 0.001 ARG S 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 691 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8086 (ttmm) REVERT: A 275 ARG cc_start: 0.7704 (tmm160) cc_final: 0.6829 (tpp80) REVERT: A 362 LYS cc_start: 0.7901 (mptt) cc_final: 0.7632 (mmtt) REVERT: A 416 GLN cc_start: 0.7830 (tp40) cc_final: 0.7513 (tp-100) REVERT: A 456 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 539 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8409 (mppt) REVERT: A 566 LYS cc_start: 0.8045 (tttp) cc_final: 0.7754 (ttmp) REVERT: B 49 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7754 (tmtt) REVERT: D 107 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7510 (ttpp) REVERT: E 131 GLU cc_start: 0.8057 (tp30) cc_final: 0.7801 (mm-30) REVERT: E 140 MET cc_start: 0.9114 (ttm) cc_final: 0.8913 (ttm) REVERT: E 270 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6954 (mp0) REVERT: F 209 GLU cc_start: 0.8058 (tt0) cc_final: 0.7835 (tp30) REVERT: F 213 GLN cc_start: 0.7605 (mt0) cc_final: 0.7361 (mt0) REVERT: G 269 GLN cc_start: 0.7509 (mm110) cc_final: 0.7072 (mt0) REVERT: G 273 LYS cc_start: 0.8433 (ptmm) cc_final: 0.8033 (pttp) REVERT: H 209 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: H 261 LYS cc_start: 0.8053 (mptt) cc_final: 0.7460 (mptm) REVERT: I 114 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7835 (mtpp) REVERT: J 78 LYS cc_start: 0.7665 (mmmm) cc_final: 0.7321 (mmmt) REVERT: J 196 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8187 (t80) REVERT: J 206 ASN cc_start: 0.8245 (m-40) cc_final: 0.7924 (m-40) REVERT: K 149 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8096 (mp) REVERT: K 175 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8029 (ttt90) REVERT: K 196 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8796 (t80) REVERT: L 76 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7496 (mtp180) REVERT: L 225 LYS cc_start: 0.7994 (pptt) cc_final: 0.7672 (ptmm) REVERT: M 175 ARG cc_start: 0.7472 (tpt-90) cc_final: 0.7233 (tpt170) REVERT: M 184 GLU cc_start: 0.7969 (tt0) cc_final: 0.7550 (pt0) REVERT: M 205 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7454 (mttt) REVERT: M 211 TRP cc_start: 0.7596 (t-100) cc_final: 0.7273 (t-100) REVERT: N 275 TYR cc_start: 0.6941 (m-80) cc_final: 0.6512 (m-80) REVERT: O 152 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: O 229 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.4916 (mtp) REVERT: O 273 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7618 (mtmt) REVERT: P 182 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6784 (mtp180) REVERT: Q 128 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6420 (tpt170) REVERT: Q 214 MET cc_start: 0.4821 (mpt) cc_final: 0.4549 (mpp) REVERT: Q 229 MET cc_start: 0.3095 (mpt) cc_final: 0.1811 (tpp) REVERT: Q 250 GLU cc_start: 0.5164 (tp30) cc_final: 0.3881 (pt0) REVERT: R 104 LYS cc_start: 0.7645 (mttt) cc_final: 0.6824 (ttmm) REVERT: R 165 GLU cc_start: 0.8578 (tp30) cc_final: 0.8239 (tp30) REVERT: R 166 LYS cc_start: 0.8351 (mmpt) cc_final: 0.8123 (mmpt) REVERT: R 188 ARG cc_start: 0.7684 (ttm170) cc_final: 0.6813 (tmm160) REVERT: R 345 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7636 (mm-30) REVERT: R 381 MET cc_start: 0.8642 (mmm) cc_final: 0.8285 (mmm) REVERT: R 434 GLU cc_start: 0.8235 (pt0) cc_final: 0.8012 (pt0) REVERT: R 465 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8167 (mm110) REVERT: S 76 LEU cc_start: 0.7212 (pt) cc_final: 0.6650 (tt) REVERT: S 295 ASN cc_start: 0.7984 (m-40) cc_final: 0.7702 (m-40) REVERT: S 349 ASP cc_start: 0.6738 (t70) cc_final: 0.6453 (t0) REVERT: S 471 ARG cc_start: 0.7567 (ppp80) cc_final: 0.7248 (ttp80) REVERT: T 373 TYR cc_start: 0.5432 (OUTLIER) cc_final: 0.4405 (t80) REVERT: U 238 MET cc_start: 0.2720 (ptm) cc_final: 0.1835 (pmm) REVERT: U 245 ASP cc_start: 0.7121 (t0) cc_final: 0.6627 (t0) REVERT: U 434 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: U 473 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5698 (m90) REVERT: r 575 TYR cc_start: 0.2875 (OUTLIER) cc_final: 0.1919 (m-80) REVERT: s 575 TYR cc_start: 0.3508 (OUTLIER) cc_final: 0.3209 (t80) REVERT: t 575 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.3415 (m-80) outliers start: 137 outliers final: 46 residues processed: 775 average time/residue: 1.7422 time to fit residues: 1658.1513 Evaluate side-chains 696 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 631 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain s residue 575 TYR Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 50.0000 chunk 440 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 393 optimal weight: 4.9990 chunk 587 optimal weight: 6.9990 chunk 622 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 557 optimal weight: 0.3980 chunk 167 optimal weight: 30.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN B 47 ASN C 33 ASN C 93 GLN C 135 ASN F 269 GLN G 206 ASN J 38 GLN K 206 ASN N 81 GLN Q 81 GLN R 113 ASN T 465 GLN U 295 ASN U 475 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 62692 Z= 0.228 Angle : 0.597 11.503 86986 Z= 0.324 Chirality : 0.041 0.300 9900 Planarity : 0.005 0.070 9171 Dihedral : 21.877 179.808 14222 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.78 % Allowed : 13.68 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 6033 helix: 1.09 (0.09), residues: 3341 sheet: -0.29 (0.21), residues: 502 loop : 0.30 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 225 HIS 0.007 0.001 HIS T 296 PHE 0.018 0.001 PHE S 306 TYR 0.019 0.001 TYR R 233 ARG 0.013 0.000 ARG S 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 674 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7682 (tmm160) cc_final: 0.6822 (tpp80) REVERT: A 362 LYS cc_start: 0.7872 (mptt) cc_final: 0.7660 (mmtt) REVERT: A 416 GLN cc_start: 0.7809 (tp40) cc_final: 0.7504 (tp-100) REVERT: A 456 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: A 492 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7475 (ttp80) REVERT: A 539 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8398 (mppt) REVERT: A 551 MET cc_start: 0.8085 (mmm) cc_final: 0.7825 (mmm) REVERT: B 49 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: B 76 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7572 (mtt90) REVERT: D 107 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7466 (ttpp) REVERT: E 131 GLU cc_start: 0.8049 (tp30) cc_final: 0.7815 (mm-30) REVERT: E 270 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6948 (mp0) REVERT: G 269 GLN cc_start: 0.7551 (mm110) cc_final: 0.7066 (mt0) REVERT: H 261 LYS cc_start: 0.8074 (mptt) cc_final: 0.7473 (mptm) REVERT: I 114 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7793 (mtpp) REVERT: J 78 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7317 (mmmt) REVERT: J 196 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8175 (t80) REVERT: J 206 ASN cc_start: 0.8187 (m-40) cc_final: 0.7740 (m110) REVERT: K 175 ARG cc_start: 0.8338 (ttm170) cc_final: 0.8073 (ttp80) REVERT: K 196 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8766 (t80) REVERT: K 225 LYS cc_start: 0.7541 (ttpm) cc_final: 0.7274 (ttmt) REVERT: L 76 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: L 225 LYS cc_start: 0.8044 (pptt) cc_final: 0.7640 (ptmm) REVERT: M 175 ARG cc_start: 0.7436 (tpt-90) cc_final: 0.7180 (tpt90) REVERT: M 184 GLU cc_start: 0.7970 (tt0) cc_final: 0.7562 (pt0) REVERT: M 205 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7457 (mttt) REVERT: M 209 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: M 211 TRP cc_start: 0.7631 (t-100) cc_final: 0.7260 (t-100) REVERT: N 275 TYR cc_start: 0.6828 (m-80) cc_final: 0.6492 (m-80) REVERT: O 152 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: O 210 MET cc_start: 0.7023 (mtp) cc_final: 0.6655 (mtt) REVERT: O 229 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.5021 (mtp) REVERT: O 273 LYS cc_start: 0.8429 (ttpt) cc_final: 0.7527 (ttmt) REVERT: P 182 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6752 (mtp180) REVERT: Q 214 MET cc_start: 0.4852 (mpt) cc_final: 0.4649 (mpp) REVERT: Q 229 MET cc_start: 0.3050 (mpt) cc_final: 0.1795 (tpp) REVERT: R 104 LYS cc_start: 0.7677 (mttt) cc_final: 0.6863 (tttp) REVERT: R 165 GLU cc_start: 0.8607 (tp30) cc_final: 0.8315 (tp30) REVERT: R 166 LYS cc_start: 0.8324 (mmpt) cc_final: 0.8116 (mmpt) REVERT: R 188 ARG cc_start: 0.7697 (ttm170) cc_final: 0.6839 (tmm160) REVERT: R 345 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7581 (mm-30) REVERT: R 381 MET cc_start: 0.8628 (mmm) cc_final: 0.8291 (mmm) REVERT: R 434 GLU cc_start: 0.8285 (pt0) cc_final: 0.7990 (pt0) REVERT: R 465 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8158 (mm110) REVERT: S 76 LEU cc_start: 0.7234 (pt) cc_final: 0.6670 (tt) REVERT: S 295 ASN cc_start: 0.7927 (m-40) cc_final: 0.7637 (m-40) REVERT: S 349 ASP cc_start: 0.6842 (t70) cc_final: 0.6542 (t0) REVERT: S 430 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: T 373 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4633 (t80) REVERT: T 411 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6887 (mtm) REVERT: U 238 MET cc_start: 0.2758 (ptm) cc_final: 0.1855 (pmm) REVERT: U 245 ASP cc_start: 0.7154 (t0) cc_final: 0.6526 (t0) REVERT: U 434 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: U 473 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5679 (m90) REVERT: r 575 TYR cc_start: 0.2969 (OUTLIER) cc_final: 0.2032 (m-80) REVERT: r 582 TYR cc_start: 0.3175 (OUTLIER) cc_final: 0.2849 (t80) REVERT: s 575 TYR cc_start: 0.3438 (OUTLIER) cc_final: 0.3221 (t80) outliers start: 148 outliers final: 56 residues processed: 765 average time/residue: 1.7703 time to fit residues: 1667.7647 Evaluate side-chains 700 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 626 time to evaluate : 4.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 261 LYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 351 GLU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 411 MET Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 286 THR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain s residue 575 TYR Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 0.4980 chunk 353 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 chunk 531 optimal weight: 6.9990 chunk 430 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 558 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN C 93 GLN C 135 ASN D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 22 GLN J 38 GLN K 206 ASN N 81 GLN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN R 295 ASN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 427 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 62692 Z= 0.318 Angle : 0.643 11.604 86986 Z= 0.346 Chirality : 0.044 0.335 9900 Planarity : 0.005 0.082 9171 Dihedral : 21.941 179.875 14222 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.29 % Allowed : 14.34 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 6033 helix: 1.00 (0.09), residues: 3342 sheet: -0.39 (0.21), residues: 488 loop : 0.20 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 225 HIS 0.011 0.001 HIS L 77 PHE 0.027 0.002 PHE S 306 TYR 0.029 0.002 TYR R 233 ARG 0.015 0.001 ARG S 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 655 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8119 (ttmm) REVERT: A 275 ARG cc_start: 0.7668 (tmm160) cc_final: 0.6813 (tpp80) REVERT: A 362 LYS cc_start: 0.7909 (mptt) cc_final: 0.7674 (mmtt) REVERT: A 416 GLN cc_start: 0.7839 (tp40) cc_final: 0.7518 (tp-100) REVERT: A 456 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: A 470 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7664 (ptmm) REVERT: A 539 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8402 (mppt) REVERT: B 20 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: B 49 LYS cc_start: 0.8849 (mtmm) cc_final: 0.7754 (tmtt) REVERT: C 156 MET cc_start: 0.8900 (ttt) cc_final: 0.8619 (ttt) REVERT: D 107 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7471 (ttpp) REVERT: D 265 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7059 (tptt) REVERT: E 76 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6109 (ttp-170) REVERT: E 131 GLU cc_start: 0.8071 (tp30) cc_final: 0.7847 (mm-30) REVERT: E 270 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6971 (mp0) REVERT: F 74 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7587 (ppt-90) REVERT: G 269 GLN cc_start: 0.7558 (mm110) cc_final: 0.7092 (mt0) REVERT: G 273 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7837 (pttm) REVERT: H 261 LYS cc_start: 0.8066 (mptt) cc_final: 0.7481 (mptm) REVERT: I 114 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7838 (mtpp) REVERT: J 78 LYS cc_start: 0.7693 (mmmm) cc_final: 0.7331 (mmmt) REVERT: J 196 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8177 (t80) REVERT: J 206 ASN cc_start: 0.8240 (m-40) cc_final: 0.7961 (m-40) REVERT: J 243 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8469 (mtt180) REVERT: K 149 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8203 (mp) REVERT: K 175 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8050 (ttp80) REVERT: K 196 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8803 (t80) REVERT: K 214 MET cc_start: 0.8465 (mtp) cc_final: 0.8053 (mtt) REVERT: L 76 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7522 (mtp180) REVERT: L 225 LYS cc_start: 0.8077 (pptt) cc_final: 0.7754 (ptmm) REVERT: M 175 ARG cc_start: 0.7450 (tpt-90) cc_final: 0.7175 (tpt90) REVERT: M 184 GLU cc_start: 0.7997 (tt0) cc_final: 0.7638 (pt0) REVERT: M 205 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7461 (mttt) REVERT: M 211 TRP cc_start: 0.7651 (t-100) cc_final: 0.7270 (t-100) REVERT: M 223 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5630 (m110) REVERT: N 275 TYR cc_start: 0.6946 (m-80) cc_final: 0.6630 (m-80) REVERT: O 71 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: O 210 MET cc_start: 0.7130 (mtp) cc_final: 0.6641 (mtt) REVERT: O 229 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5016 (mtp) REVERT: O 273 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7521 (mtmt) REVERT: P 182 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6806 (mtp180) REVERT: Q 128 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6511 (tpt170) REVERT: Q 214 MET cc_start: 0.4856 (mpt) cc_final: 0.4587 (mpp) REVERT: Q 229 MET cc_start: 0.3092 (mpt) cc_final: 0.1816 (tpp) REVERT: R 165 GLU cc_start: 0.8658 (tp30) cc_final: 0.8407 (tp30) REVERT: R 188 ARG cc_start: 0.7658 (ttm170) cc_final: 0.6788 (tmm160) REVERT: R 345 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7639 (mm-30) REVERT: R 381 MET cc_start: 0.8667 (mmm) cc_final: 0.8357 (mmm) REVERT: R 434 GLU cc_start: 0.8317 (pt0) cc_final: 0.8028 (pt0) REVERT: S 76 LEU cc_start: 0.7235 (pt) cc_final: 0.6684 (tt) REVERT: S 295 ASN cc_start: 0.7974 (m-40) cc_final: 0.7693 (m-40) REVERT: S 349 ASP cc_start: 0.6937 (t70) cc_final: 0.6671 (t0) REVERT: S 375 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: S 427 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5276 (mp-120) REVERT: S 430 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7570 (mmm) REVERT: S 431 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.4542 (t80) REVERT: S 470 THR cc_start: 0.7196 (t) cc_final: 0.6939 (p) REVERT: T 355 ARG cc_start: 0.7904 (tmm160) cc_final: 0.7575 (tpt90) REVERT: T 373 TYR cc_start: 0.5437 (OUTLIER) cc_final: 0.4749 (t80) REVERT: T 434 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: U 201 VAL cc_start: 0.5303 (OUTLIER) cc_final: 0.5005 (t) REVERT: U 225 TRP cc_start: 0.6478 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: U 238 MET cc_start: 0.2962 (ptm) cc_final: 0.1993 (pmm) REVERT: U 300 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8331 (mp) REVERT: U 372 ARG cc_start: 0.6379 (ttp80) cc_final: 0.5728 (ttp-110) REVERT: U 403 GLU cc_start: 0.6607 (tp30) cc_final: 0.6403 (mm-30) REVERT: U 434 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7035 (pm20) REVERT: U 473 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.5697 (m90) REVERT: r 575 TYR cc_start: 0.2990 (OUTLIER) cc_final: 0.2053 (m-80) REVERT: r 582 TYR cc_start: 0.3079 (OUTLIER) cc_final: 0.1412 (m-80) REVERT: s 575 TYR cc_start: 0.3547 (OUTLIER) cc_final: 0.3243 (t80) outliers start: 175 outliers final: 73 residues processed: 771 average time/residue: 1.8643 time to fit residues: 1802.8754 Evaluate side-chains 736 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 630 time to evaluate : 5.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 261 LYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 264 ASP Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 223 ASN Chi-restraints excluded: chain M residue 243 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain O residue 273 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 351 GLU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain S residue 431 TYR Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 286 THR Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain s residue 575 TYR Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 4.9990 chunk 560 optimal weight: 1.9990 chunk 123 optimal weight: 0.0060 chunk 365 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 623 optimal weight: 0.0870 chunk 517 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 overall best weight: 1.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 442 GLN B 80 GLN C 135 ASN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN N 81 GLN Q 43 HIS Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 62692 Z= 0.164 Angle : 0.560 12.502 86986 Z= 0.303 Chirality : 0.039 0.271 9900 Planarity : 0.004 0.054 9171 Dihedral : 21.783 179.671 14222 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.16 % Allowed : 16.12 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 6033 helix: 1.40 (0.09), residues: 3334 sheet: -0.12 (0.22), residues: 474 loop : 0.32 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP T 225 HIS 0.031 0.001 HIS S 473 PHE 0.013 0.001 PHE A 13 TYR 0.017 0.001 TYR T 459 ARG 0.017 0.000 ARG U 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 700 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7637 (tmm160) cc_final: 0.6750 (tpp80) REVERT: A 362 LYS cc_start: 0.7836 (mptt) cc_final: 0.7613 (mmtt) REVERT: A 416 GLN cc_start: 0.7766 (tp40) cc_final: 0.7491 (tp-100) REVERT: A 486 GLU cc_start: 0.7748 (pm20) cc_final: 0.7411 (pm20) REVERT: A 492 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7467 (ttp80) REVERT: A 539 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8387 (mppt) REVERT: A 551 MET cc_start: 0.8020 (mmm) cc_final: 0.7791 (mmm) REVERT: B 49 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.7771 (tmtt) REVERT: C 123 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7900 (p0) REVERT: C 147 GLU cc_start: 0.8283 (tt0) cc_final: 0.7981 (tt0) REVERT: D 107 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7437 (ttpp) REVERT: D 265 LYS cc_start: 0.7511 (ttmm) cc_final: 0.7130 (tptt) REVERT: E 131 GLU cc_start: 0.8070 (tp30) cc_final: 0.7859 (mm-30) REVERT: E 270 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6887 (mp0) REVERT: F 74 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7465 (ppt-90) REVERT: F 227 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7622 (ttpp) REVERT: G 269 GLN cc_start: 0.7585 (mm110) cc_final: 0.7116 (mt0) REVERT: H 261 LYS cc_start: 0.8091 (mptt) cc_final: 0.7491 (mptm) REVERT: J 78 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7355 (mmmt) REVERT: J 196 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8150 (t80) REVERT: J 206 ASN cc_start: 0.8194 (m-40) cc_final: 0.7755 (m110) REVERT: K 61 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7790 (mp0) REVERT: K 99 LYS cc_start: 0.8904 (mttp) cc_final: 0.8222 (mmpt) REVERT: K 175 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7991 (ttp80) REVERT: K 196 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8634 (t80) REVERT: L 21 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6980 (tm) REVERT: L 76 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: L 225 LYS cc_start: 0.8048 (pptt) cc_final: 0.7791 (ptmm) REVERT: M 184 GLU cc_start: 0.7945 (tt0) cc_final: 0.7642 (pt0) REVERT: M 205 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7445 (mttt) REVERT: M 209 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: M 211 TRP cc_start: 0.7621 (t-100) cc_final: 0.7202 (t-100) REVERT: M 223 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.5546 (m110) REVERT: M 269 GLN cc_start: 0.6610 (mt0) cc_final: 0.6195 (mp10) REVERT: M 273 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7823 (tptt) REVERT: N 119 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7648 (mtmt) REVERT: N 182 ARG cc_start: 0.7559 (mtm180) cc_final: 0.7318 (mtm180) REVERT: N 206 ASN cc_start: 0.6903 (m-40) cc_final: 0.6643 (t0) REVERT: N 275 TYR cc_start: 0.6800 (m-80) cc_final: 0.6470 (m-80) REVERT: O 229 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5063 (mtp) REVERT: O 273 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7398 (ttmt) REVERT: P 182 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6757 (mtp180) REVERT: P 205 LYS cc_start: 0.7069 (mtpt) cc_final: 0.6672 (mmmt) REVERT: Q 214 MET cc_start: 0.4921 (mpt) cc_final: 0.4708 (mpp) REVERT: Q 229 MET cc_start: 0.3077 (mpt) cc_final: 0.1791 (tpp) REVERT: R 165 GLU cc_start: 0.8628 (tp30) cc_final: 0.8307 (tp30) REVERT: R 166 LYS cc_start: 0.8357 (mmpt) cc_final: 0.8132 (mmpt) REVERT: R 188 ARG cc_start: 0.7674 (ttm170) cc_final: 0.6813 (tmm160) REVERT: R 345 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7472 (mm-30) REVERT: R 381 MET cc_start: 0.8687 (mmm) cc_final: 0.8420 (mmm) REVERT: R 420 ARG cc_start: 0.8166 (tmm160) cc_final: 0.7675 (tmt-80) REVERT: S 76 LEU cc_start: 0.7196 (pt) cc_final: 0.6685 (tt) REVERT: S 295 ASN cc_start: 0.7885 (m-40) cc_final: 0.7651 (m-40) REVERT: S 349 ASP cc_start: 0.6897 (t70) cc_final: 0.6695 (t0) REVERT: S 430 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: T 373 TYR cc_start: 0.5579 (OUTLIER) cc_final: 0.4942 (t80) REVERT: T 434 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: U 201 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.5054 (t) REVERT: U 238 MET cc_start: 0.2966 (ptm) cc_final: 0.2197 (pmm) REVERT: U 300 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8301 (mp) REVERT: U 434 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: U 473 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5631 (m90) REVERT: r 575 TYR cc_start: 0.2962 (OUTLIER) cc_final: 0.2049 (m-80) outliers start: 115 outliers final: 43 residues processed: 772 average time/residue: 1.7426 time to fit residues: 1660.8048 Evaluate side-chains 698 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 634 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 223 ASN Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain O residue 273 LYS Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 455 optimal weight: 30.0000 chunk 352 optimal weight: 2.9990 chunk 524 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 620 optimal weight: 0.3980 chunk 388 optimal weight: 0.2980 chunk 378 optimal weight: 30.0000 chunk 286 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 620 HIS C 135 ASN D 269 GLN F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN J 38 GLN K 206 ASN N 213 GLN Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 62692 Z= 0.195 Angle : 0.573 12.836 86986 Z= 0.308 Chirality : 0.040 0.291 9900 Planarity : 0.004 0.053 9171 Dihedral : 21.775 179.972 14222 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.31 % Allowed : 16.42 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 6033 helix: 1.41 (0.09), residues: 3344 sheet: -0.14 (0.22), residues: 478 loop : 0.35 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 225 HIS 0.006 0.001 HIS L 77 PHE 0.023 0.001 PHE T 332 TYR 0.020 0.001 TYR T 459 ARG 0.011 0.000 ARG U 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 669 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7640 (tmm160) cc_final: 0.6756 (tpp80) REVERT: A 362 LYS cc_start: 0.7838 (mptt) cc_final: 0.7592 (mmtt) REVERT: A 416 GLN cc_start: 0.7788 (tp40) cc_final: 0.7515 (tp-100) REVERT: A 492 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7466 (ttp80) REVERT: A 539 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8376 (mppt) REVERT: A 551 MET cc_start: 0.8047 (mmm) cc_final: 0.7820 (mmm) REVERT: B 20 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: B 49 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7735 (tmtt) REVERT: B 76 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7603 (mtt90) REVERT: C 147 GLU cc_start: 0.8275 (tt0) cc_final: 0.7976 (tt0) REVERT: D 107 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7427 (ttpp) REVERT: E 131 GLU cc_start: 0.8100 (tp30) cc_final: 0.7890 (mm-30) REVERT: E 225 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6478 (tptp) REVERT: E 270 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6885 (mp0) REVERT: F 74 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7478 (ppt-90) REVERT: G 269 GLN cc_start: 0.7586 (mm110) cc_final: 0.7117 (mt0) REVERT: G 273 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7743 (pttm) REVERT: H 261 LYS cc_start: 0.8085 (mptt) cc_final: 0.7493 (mptm) REVERT: I 114 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7731 (mtpp) REVERT: J 78 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7349 (mmmt) REVERT: J 196 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8161 (t80) REVERT: J 206 ASN cc_start: 0.8206 (m-40) cc_final: 0.7770 (m110) REVERT: K 99 LYS cc_start: 0.8911 (mttp) cc_final: 0.8217 (mmpt) REVERT: K 175 ARG cc_start: 0.8292 (ttm170) cc_final: 0.8037 (ttp80) REVERT: K 196 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8779 (t80) REVERT: K 214 MET cc_start: 0.8367 (mtp) cc_final: 0.7999 (mtt) REVERT: L 76 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7413 (mtp180) REVERT: L 225 LYS cc_start: 0.8021 (pptt) cc_final: 0.7789 (ptmm) REVERT: M 184 GLU cc_start: 0.7983 (tt0) cc_final: 0.7656 (pt0) REVERT: M 194 LEU cc_start: 0.8905 (tp) cc_final: 0.8694 (tt) REVERT: M 205 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7451 (mttt) REVERT: M 211 TRP cc_start: 0.7651 (t-100) cc_final: 0.7236 (t-100) REVERT: M 223 ASN cc_start: 0.5903 (OUTLIER) cc_final: 0.5583 (m110) REVERT: M 269 GLN cc_start: 0.6613 (mt0) cc_final: 0.6243 (mp10) REVERT: M 273 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7820 (tptt) REVERT: N 119 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7676 (mtmt) REVERT: N 275 TYR cc_start: 0.6828 (m-80) cc_final: 0.6554 (m-80) REVERT: O 152 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: O 210 MET cc_start: 0.6998 (mtp) cc_final: 0.6523 (mtt) REVERT: O 229 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.4867 (mtp) REVERT: O 231 ARG cc_start: 0.6831 (ttt180) cc_final: 0.6452 (mtt-85) REVERT: P 182 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6770 (mtp180) REVERT: P 205 LYS cc_start: 0.7083 (mtpt) cc_final: 0.6703 (mmmt) REVERT: Q 128 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6474 (tpt170) REVERT: Q 229 MET cc_start: 0.3027 (mpt) cc_final: 0.1812 (tpp) REVERT: Q 262 LYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4318 (ptmm) REVERT: R 165 GLU cc_start: 0.8664 (tp30) cc_final: 0.8325 (tp30) REVERT: R 166 LYS cc_start: 0.8392 (mmpt) cc_final: 0.8161 (mmpt) REVERT: R 188 ARG cc_start: 0.7657 (ttm170) cc_final: 0.6792 (tmm160) REVERT: R 316 GLU cc_start: 0.7838 (mp0) cc_final: 0.7532 (mp0) REVERT: R 345 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7526 (mm-30) REVERT: R 381 MET cc_start: 0.8711 (mmm) cc_final: 0.8379 (mmm) REVERT: R 420 ARG cc_start: 0.8206 (tmm160) cc_final: 0.7650 (tmt-80) REVERT: R 434 GLU cc_start: 0.8283 (pt0) cc_final: 0.8053 (pt0) REVERT: S 76 LEU cc_start: 0.7192 (pt) cc_final: 0.6684 (tt) REVERT: S 139 GLU cc_start: 0.8645 (mp0) cc_final: 0.8432 (mm-30) REVERT: S 295 ASN cc_start: 0.7870 (m-40) cc_final: 0.7631 (m-40) REVERT: S 430 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: S 471 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.6647 (tmt-80) REVERT: T 238 MET cc_start: 0.5766 (mpp) cc_final: 0.5544 (mpp) REVERT: T 373 TYR cc_start: 0.5609 (OUTLIER) cc_final: 0.5112 (t80) REVERT: U 201 VAL cc_start: 0.5311 (OUTLIER) cc_final: 0.5043 (t) REVERT: U 238 MET cc_start: 0.2961 (ptm) cc_final: 0.2331 (pmm) REVERT: U 300 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8295 (mp) REVERT: U 372 ARG cc_start: 0.6375 (ttp80) cc_final: 0.5771 (ttp-110) REVERT: U 434 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: U 473 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.5631 (m90) REVERT: r 575 TYR cc_start: 0.2957 (OUTLIER) cc_final: 0.2033 (m-80) REVERT: r 582 TYR cc_start: 0.2913 (OUTLIER) cc_final: 0.1407 (m-80) outliers start: 123 outliers final: 54 residues processed: 746 average time/residue: 1.7157 time to fit residues: 1579.9310 Evaluate side-chains 714 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 636 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 225 LYS Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 223 ASN Chi-restraints excluded: chain M residue 243 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 262 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 445 ASN Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 370 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 120 optimal weight: 0.0470 chunk 394 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 487 optimal weight: 9.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 620 HIS C 33 ASN C 135 ASN D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN N 213 GLN Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 133 GLN T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 62692 Z= 0.240 Angle : 0.602 19.635 86986 Z= 0.322 Chirality : 0.041 0.307 9900 Planarity : 0.005 0.060 9171 Dihedral : 21.808 179.704 14222 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 16.67 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 6033 helix: 1.33 (0.09), residues: 3348 sheet: -0.14 (0.22), residues: 479 loop : 0.30 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP U 225 HIS 0.008 0.001 HIS L 77 PHE 0.022 0.001 PHE T 332 TYR 0.022 0.002 TYR R 233 ARG 0.011 0.000 ARG U 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 653 time to evaluate : 4.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7656 (tmm160) cc_final: 0.6778 (tpp80) REVERT: A 362 LYS cc_start: 0.7817 (mptt) cc_final: 0.7596 (mmtt) REVERT: A 416 GLN cc_start: 0.7806 (tp40) cc_final: 0.7524 (tp-100) REVERT: A 492 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7482 (ttp80) REVERT: A 539 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8387 (mppt) REVERT: A 551 MET cc_start: 0.8061 (mmm) cc_final: 0.7827 (mmm) REVERT: B 20 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 49 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7740 (tmtt) REVERT: B 76 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7638 (mtt90) REVERT: C 147 GLU cc_start: 0.8274 (tt0) cc_final: 0.7977 (tt0) REVERT: C 156 MET cc_start: 0.8937 (ttt) cc_final: 0.8705 (ttt) REVERT: D 107 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7427 (ttpp) REVERT: E 131 GLU cc_start: 0.8069 (tp30) cc_final: 0.7853 (mm-30) REVERT: E 270 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6926 (mp0) REVERT: F 74 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7509 (ppt-90) REVERT: G 269 GLN cc_start: 0.7586 (mm110) cc_final: 0.7109 (mt0) REVERT: G 273 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7760 (pttm) REVERT: H 261 LYS cc_start: 0.8081 (mptt) cc_final: 0.7501 (mptm) REVERT: I 114 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7755 (mtpp) REVERT: J 78 LYS cc_start: 0.7675 (mmmm) cc_final: 0.7334 (mmmt) REVERT: J 196 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8184 (t80) REVERT: J 206 ASN cc_start: 0.8189 (m-40) cc_final: 0.7749 (m110) REVERT: K 99 LYS cc_start: 0.8922 (mttp) cc_final: 0.8222 (mmpt) REVERT: K 175 ARG cc_start: 0.8332 (ttm170) cc_final: 0.7990 (ttp80) REVERT: K 196 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8760 (t80) REVERT: L 76 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: L 149 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8505 (mp) REVERT: L 225 LYS cc_start: 0.8014 (pptt) cc_final: 0.7777 (ptmm) REVERT: M 184 GLU cc_start: 0.8007 (tt0) cc_final: 0.7643 (pt0) REVERT: M 194 LEU cc_start: 0.8908 (tp) cc_final: 0.8698 (tt) REVERT: M 205 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7472 (mttt) REVERT: M 211 TRP cc_start: 0.7648 (t-100) cc_final: 0.7229 (t-100) REVERT: M 223 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5555 (m110) REVERT: M 269 GLN cc_start: 0.6722 (mt0) cc_final: 0.6363 (mp10) REVERT: N 119 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7719 (mtmt) REVERT: N 199 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7179 (mt) REVERT: O 152 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: O 210 MET cc_start: 0.7010 (mtp) cc_final: 0.6597 (mtt) REVERT: O 229 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.4888 (mtp) REVERT: P 182 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6786 (mtp180) REVERT: Q 128 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6511 (tpt170) REVERT: Q 229 MET cc_start: 0.3040 (mpt) cc_final: 0.1836 (tpp) REVERT: Q 262 LYS cc_start: 0.4707 (OUTLIER) cc_final: 0.4339 (ptmm) REVERT: R 165 GLU cc_start: 0.8670 (tp30) cc_final: 0.8311 (tp30) REVERT: R 166 LYS cc_start: 0.8393 (mmpt) cc_final: 0.8161 (mmpt) REVERT: R 188 ARG cc_start: 0.7673 (ttm170) cc_final: 0.6802 (tmm160) REVERT: R 312 ASP cc_start: 0.6695 (t0) cc_final: 0.6429 (t0) REVERT: R 345 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7573 (mm-30) REVERT: R 381 MET cc_start: 0.8707 (mmm) cc_final: 0.8412 (mmm) REVERT: R 416 ARG cc_start: 0.5445 (OUTLIER) cc_final: 0.4540 (mtt90) REVERT: R 420 ARG cc_start: 0.8162 (tmm160) cc_final: 0.7659 (tmt-80) REVERT: R 434 GLU cc_start: 0.8314 (pt0) cc_final: 0.8056 (pt0) REVERT: S 76 LEU cc_start: 0.7208 (pt) cc_final: 0.6691 (tt) REVERT: S 295 ASN cc_start: 0.7931 (m-40) cc_final: 0.7698 (m-40) REVERT: S 381 MET cc_start: 0.8133 (ttp) cc_final: 0.7916 (ppp) REVERT: S 430 MET cc_start: 0.8111 (mpp) cc_final: 0.7835 (mmm) REVERT: S 471 ARG cc_start: 0.7461 (ptm-80) cc_final: 0.6625 (tmt-80) REVERT: T 238 MET cc_start: 0.5762 (mpp) cc_final: 0.5436 (mmt) REVERT: T 373 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.5197 (t80) REVERT: T 434 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: U 201 VAL cc_start: 0.5188 (OUTLIER) cc_final: 0.4916 (t) REVERT: U 238 MET cc_start: 0.3007 (ptm) cc_final: 0.2376 (pmm) REVERT: U 300 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8233 (mp) REVERT: U 360 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: U 434 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: U 473 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5678 (m90) REVERT: r 575 TYR cc_start: 0.2961 (OUTLIER) cc_final: 0.2042 (m-80) REVERT: r 582 TYR cc_start: 0.3021 (OUTLIER) cc_final: 0.1425 (m-80) outliers start: 131 outliers final: 65 residues processed: 737 average time/residue: 1.7670 time to fit residues: 1606.6249 Evaluate side-chains 724 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 632 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 223 ASN Chi-restraints excluded: chain M residue 243 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 262 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 416 ARG Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 445 ASN Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 507 LEU Chi-restraints excluded: chain T residue 521 LYS Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 20.0000 chunk 594 optimal weight: 20.0000 chunk 542 optimal weight: 20.0000 chunk 578 optimal weight: 0.0370 chunk 348 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 454 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 522 optimal weight: 20.0000 chunk 547 optimal weight: 5.9990 chunk 576 optimal weight: 50.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 620 HIS C 135 ASN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 62692 Z= 0.249 Angle : 0.617 17.610 86986 Z= 0.329 Chirality : 0.042 0.310 9900 Planarity : 0.005 0.057 9171 Dihedral : 21.832 179.511 14222 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.22 % Allowed : 17.04 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 6033 helix: 1.29 (0.09), residues: 3345 sheet: -0.17 (0.22), residues: 479 loop : 0.27 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 86 HIS 0.008 0.001 HIS L 77 PHE 0.022 0.002 PHE T 332 TYR 0.022 0.002 TYR R 233 ARG 0.015 0.000 ARG S 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 654 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7650 (tmm160) cc_final: 0.6775 (tpp80) REVERT: A 362 LYS cc_start: 0.7840 (mptt) cc_final: 0.7614 (mmtt) REVERT: A 416 GLN cc_start: 0.7808 (tp40) cc_final: 0.7515 (tp-100) REVERT: A 492 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7485 (ttp80) REVERT: A 539 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8389 (mppt) REVERT: B 20 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: B 49 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.7753 (tmtt) REVERT: B 76 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7635 (mtt90) REVERT: C 147 GLU cc_start: 0.8261 (tt0) cc_final: 0.7957 (tt0) REVERT: D 107 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7424 (ttpp) REVERT: E 131 GLU cc_start: 0.8050 (tp30) cc_final: 0.7834 (mm-30) REVERT: E 270 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6932 (mp0) REVERT: F 74 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7518 (ppt-90) REVERT: G 269 GLN cc_start: 0.7593 (mm110) cc_final: 0.7120 (mt0) REVERT: G 273 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7750 (pttm) REVERT: H 261 LYS cc_start: 0.8088 (mptt) cc_final: 0.7506 (mptm) REVERT: I 114 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7754 (mtpp) REVERT: J 78 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7338 (mmmt) REVERT: J 196 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8183 (t80) REVERT: J 206 ASN cc_start: 0.8220 (m-40) cc_final: 0.7779 (m110) REVERT: K 99 LYS cc_start: 0.8923 (mttp) cc_final: 0.8220 (mmpt) REVERT: K 175 ARG cc_start: 0.8337 (ttm170) cc_final: 0.8005 (ttp80) REVERT: K 196 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8768 (t80) REVERT: L 76 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7427 (mtp180) REVERT: L 149 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8509 (mp) REVERT: L 225 LYS cc_start: 0.8025 (pptt) cc_final: 0.7783 (ptmm) REVERT: M 184 GLU cc_start: 0.8032 (tt0) cc_final: 0.7681 (pt0) REVERT: M 194 LEU cc_start: 0.8908 (tp) cc_final: 0.8702 (tt) REVERT: M 205 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7464 (mttt) REVERT: M 211 TRP cc_start: 0.7659 (t-100) cc_final: 0.7240 (t-100) REVERT: M 223 ASN cc_start: 0.5919 (OUTLIER) cc_final: 0.5594 (m110) REVERT: M 269 GLN cc_start: 0.6722 (mt0) cc_final: 0.6404 (mp10) REVERT: M 270 GLU cc_start: 0.7594 (pt0) cc_final: 0.7367 (pt0) REVERT: M 273 LYS cc_start: 0.8064 (ttpp) cc_final: 0.7766 (tptt) REVERT: N 119 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7722 (mtmt) REVERT: O 152 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: O 210 MET cc_start: 0.7071 (mtp) cc_final: 0.6712 (mtt) REVERT: O 229 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.4896 (mtp) REVERT: P 182 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6773 (mtp180) REVERT: P 205 LYS cc_start: 0.7174 (mtpt) cc_final: 0.6733 (mmmt) REVERT: Q 128 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6509 (tpt170) REVERT: Q 214 MET cc_start: 0.4423 (mpp) cc_final: 0.3909 (mtt) REVERT: Q 229 MET cc_start: 0.3067 (mpt) cc_final: 0.1869 (tpp) REVERT: Q 262 LYS cc_start: 0.4734 (OUTLIER) cc_final: 0.4380 (ptmm) REVERT: R 165 GLU cc_start: 0.8669 (tp30) cc_final: 0.8300 (tp30) REVERT: R 166 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8164 (mmpt) REVERT: R 188 ARG cc_start: 0.7701 (ttm170) cc_final: 0.6821 (tmm160) REVERT: R 191 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7734 (tptp) REVERT: R 312 ASP cc_start: 0.6685 (t0) cc_final: 0.6328 (t0) REVERT: R 316 GLU cc_start: 0.7852 (mp0) cc_final: 0.7546 (mp0) REVERT: R 345 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7576 (mm-30) REVERT: R 381 MET cc_start: 0.8712 (mmm) cc_final: 0.8407 (mmm) REVERT: R 416 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.4516 (mtt90) REVERT: R 420 ARG cc_start: 0.8149 (tmm160) cc_final: 0.7672 (tmt-80) REVERT: R 434 GLU cc_start: 0.8305 (pt0) cc_final: 0.8028 (pt0) REVERT: S 76 LEU cc_start: 0.7203 (pt) cc_final: 0.6701 (tt) REVERT: S 191 LYS cc_start: 0.7107 (tttp) cc_final: 0.6766 (ptmt) REVERT: S 295 ASN cc_start: 0.7883 (m-40) cc_final: 0.7675 (m-40) REVERT: S 381 MET cc_start: 0.8143 (ttp) cc_final: 0.7889 (ppp) REVERT: S 430 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: S 471 ARG cc_start: 0.7440 (ptm-80) cc_final: 0.6584 (tmt-80) REVERT: T 238 MET cc_start: 0.5766 (mpp) cc_final: 0.5332 (mmt) REVERT: T 373 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5189 (t80) REVERT: T 434 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: U 201 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4911 (t) REVERT: U 238 MET cc_start: 0.3120 (ptm) cc_final: 0.2460 (pmm) REVERT: U 325 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7383 (tptp) REVERT: U 434 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: U 473 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.5693 (m90) REVERT: r 575 TYR cc_start: 0.2941 (OUTLIER) cc_final: 0.2032 (m-80) REVERT: r 582 TYR cc_start: 0.3033 (OUTLIER) cc_final: 0.1413 (m-80) outliers start: 118 outliers final: 67 residues processed: 728 average time/residue: 1.6883 time to fit residues: 1524.0204 Evaluate side-chains 730 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 637 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 231 ARG Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 223 ASN Chi-restraints excluded: chain M residue 243 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 262 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 416 ARG Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 445 ASN Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 507 LEU Chi-restraints excluded: chain T residue 521 LYS Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 325 LYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 424 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 9.9990 chunk 611 optimal weight: 50.0000 chunk 373 optimal weight: 8.9990 chunk 290 optimal weight: 8.9990 chunk 425 optimal weight: 10.0000 chunk 641 optimal weight: 0.0370 chunk 590 optimal weight: 0.9990 chunk 510 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 442 GLN A 620 HIS C 33 ASN C 135 ASN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62692 Z= 0.200 Angle : 0.595 17.579 86986 Z= 0.318 Chirality : 0.040 0.292 9900 Planarity : 0.005 0.124 9171 Dihedral : 21.791 179.346 14222 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.01 % Allowed : 17.40 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.11), residues: 6033 helix: 1.38 (0.09), residues: 3349 sheet: -0.11 (0.22), residues: 475 loop : 0.27 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP S 86 HIS 0.009 0.001 HIS T 296 PHE 0.022 0.001 PHE T 332 TYR 0.019 0.001 TYR T 459 ARG 0.020 0.000 ARG R 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12066 Ramachandran restraints generated. 6033 Oldfield, 0 Emsley, 6033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 644 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7642 (tmm160) cc_final: 0.6759 (tpp80) REVERT: A 362 LYS cc_start: 0.7817 (mptt) cc_final: 0.7579 (mmtt) REVERT: A 416 GLN cc_start: 0.7796 (tp40) cc_final: 0.7509 (tp-100) REVERT: A 456 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: A 492 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7479 (ttp80) REVERT: A 539 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8382 (mppt) REVERT: A 547 LYS cc_start: 0.8426 (mmpt) cc_final: 0.8194 (mmmm) REVERT: A 551 MET cc_start: 0.8054 (mmm) cc_final: 0.7831 (mmm) REVERT: B 20 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 49 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7743 (tmtt) REVERT: B 76 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7617 (mtt90) REVERT: C 147 GLU cc_start: 0.8252 (tt0) cc_final: 0.7948 (tt0) REVERT: C 156 MET cc_start: 0.8948 (ttt) cc_final: 0.8687 (ttt) REVERT: D 107 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7426 (ttpp) REVERT: E 131 GLU cc_start: 0.8070 (tp30) cc_final: 0.7857 (mm-30) REVERT: E 270 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6912 (mp0) REVERT: F 74 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7490 (ppt-90) REVERT: G 269 GLN cc_start: 0.7591 (mm110) cc_final: 0.7129 (mt0) REVERT: G 273 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7730 (pttm) REVERT: H 261 LYS cc_start: 0.8094 (mptt) cc_final: 0.7510 (mptm) REVERT: I 114 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: J 78 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7378 (mmmt) REVERT: J 196 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8190 (t80) REVERT: J 206 ASN cc_start: 0.8206 (m-40) cc_final: 0.7761 (m110) REVERT: K 99 LYS cc_start: 0.8922 (mttp) cc_final: 0.8219 (mmpt) REVERT: K 175 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7976 (ttp80) REVERT: K 196 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8799 (t80) REVERT: L 76 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7409 (mtp180) REVERT: L 225 LYS cc_start: 0.8010 (pptt) cc_final: 0.7773 (ptmm) REVERT: M 128 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8578 (tpt-90) REVERT: M 184 GLU cc_start: 0.8012 (tt0) cc_final: 0.7616 (pt0) REVERT: M 194 LEU cc_start: 0.8884 (tp) cc_final: 0.8682 (tt) REVERT: M 205 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7449 (mttt) REVERT: M 211 TRP cc_start: 0.7649 (t-100) cc_final: 0.7254 (t-100) REVERT: M 269 GLN cc_start: 0.6715 (mt0) cc_final: 0.6369 (mp10) REVERT: M 270 GLU cc_start: 0.7628 (pt0) cc_final: 0.7413 (pt0) REVERT: M 273 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7728 (tptt) REVERT: N 119 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7678 (mtmt) REVERT: O 152 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: O 210 MET cc_start: 0.7040 (mtp) cc_final: 0.6751 (mtt) REVERT: O 214 MET cc_start: 0.6493 (pmt) cc_final: 0.6141 (pmm) REVERT: O 229 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4914 (mtp) REVERT: P 182 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6742 (mtp180) REVERT: P 205 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6746 (mmmt) REVERT: Q 128 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6502 (tpt170) REVERT: Q 229 MET cc_start: 0.3068 (mpt) cc_final: 0.1870 (tpp) REVERT: Q 262 LYS cc_start: 0.4708 (OUTLIER) cc_final: 0.4363 (ptmm) REVERT: R 165 GLU cc_start: 0.8657 (tp30) cc_final: 0.8243 (tp30) REVERT: R 166 LYS cc_start: 0.8389 (mmpt) cc_final: 0.8144 (mmpt) REVERT: R 188 ARG cc_start: 0.7688 (ttm170) cc_final: 0.6818 (tmm160) REVERT: R 191 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7735 (tptp) REVERT: R 312 ASP cc_start: 0.6654 (t0) cc_final: 0.6366 (t0) REVERT: R 316 GLU cc_start: 0.7842 (mp0) cc_final: 0.7546 (mp0) REVERT: R 345 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7530 (mm-30) REVERT: R 381 MET cc_start: 0.8708 (mmm) cc_final: 0.8428 (mmm) REVERT: R 416 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.4519 (mtt90) REVERT: R 420 ARG cc_start: 0.8172 (tmm160) cc_final: 0.7693 (tmt-80) REVERT: R 434 GLU cc_start: 0.8291 (pt0) cc_final: 0.8018 (pt0) REVERT: S 76 LEU cc_start: 0.7173 (pt) cc_final: 0.6678 (tt) REVERT: S 191 LYS cc_start: 0.6968 (tttp) cc_final: 0.6617 (ptmt) REVERT: S 430 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7745 (mmm) REVERT: T 199 ASN cc_start: 0.4825 (OUTLIER) cc_final: 0.4512 (t0) REVERT: T 238 MET cc_start: 0.5674 (mpp) cc_final: 0.5367 (mmt) REVERT: T 355 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6466 (tmm160) REVERT: T 373 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.5089 (t80) REVERT: T 434 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: U 201 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4913 (t) REVERT: U 238 MET cc_start: 0.3144 (ptm) cc_final: 0.2515 (pmm) REVERT: U 325 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7357 (tptp) REVERT: U 434 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: U 473 HIS cc_start: 0.6215 (OUTLIER) cc_final: 0.5675 (m90) REVERT: r 575 TYR cc_start: 0.2920 (OUTLIER) cc_final: 0.2012 (m-80) REVERT: r 582 TYR cc_start: 0.2972 (OUTLIER) cc_final: 0.1349 (m-80) outliers start: 107 outliers final: 60 residues processed: 714 average time/residue: 1.7516 time to fit residues: 1541.3743 Evaluate side-chains 722 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 635 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 231 ARG Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 243 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 262 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 416 ARG Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 445 ASN Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 384 GLN Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 430 MET Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 521 LYS Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 325 LYS Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Chi-restraints excluded: chain r residue 575 TYR Chi-restraints excluded: chain r residue 582 TYR Chi-restraints excluded: chain s residue 573 TRP Chi-restraints excluded: chain t residue 575 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 20.0000 chunk 544 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 471 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 511 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 chunk 525 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 94 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 304 HIS A 442 GLN A 620 HIS C 135 ASN D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN ** T 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151372 restraints weight = 76160.801| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.63 r_work: 0.3686 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 62692 Z= 0.336 Angle : 0.668 17.043 86986 Z= 0.355 Chirality : 0.044 0.337 9900 Planarity : 0.005 0.068 9171 Dihedral : 21.911 179.874 14222 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.09 % Allowed : 17.49 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 6033 helix: 1.12 (0.09), residues: 3349 sheet: -0.26 (0.22), residues: 476 loop : 0.15 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 86 HIS 0.010 0.001 HIS L 77 PHE 0.029 0.002 PHE S 306 TYR 0.030 0.002 TYR R 233 ARG 0.012 0.001 ARG U 493 =============================================================================== Job complete usr+sys time: 25938.74 seconds wall clock time: 442 minutes 56.38 seconds (26576.38 seconds total)