Starting phenix.real_space_refine on Wed Jun 26 06:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/06_2024/8rdu_19075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/06_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_19075/06_2024/8rdu_19075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/06_2024/8rdu_19075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/06_2024/8rdu_19075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdu_19075/06_2024/8rdu_19075_updated.pdb" } 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 Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 25.02, per 1000 atoms: 0.41 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.83 Conformation dependent library (CDL) restraints added in 6.8 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... running ksdssp... Secondary structure from input PDB file: 290 helices and 30 sheets defined 50.9% alpha, 8.8% beta 197 base pairs and 363 stacking pairs defined. Time for finding SS restraints: 22.42 Creating SS restraints... Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.532A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 Proline residue: A 65 - end of helix removed outlier: 4.360A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 114 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.729A pdb=" N GLU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 174 through 184 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) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 211 through 233 removed outlier: 3.897A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 319 through 337 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 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 405 Processing helix chain 'A' and resid 413 through 430 removed outlier: 4.537A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 507 removed outlier: 6.388A pdb=" N ASP A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 517 through 537 Processing helix chain 'A' and resid 551 through 566 removed outlier: 3.600A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 26 through 46 removed outlier: 3.566A pdb=" N ALA B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 74 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 76 through 86 Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 37 through 44 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.740A pdb=" N VAL C 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 54 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.840A pdb=" N VAL C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.557A pdb=" N MET C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 122 through 136 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.107A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) 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 174 through 182 removed outlier: 4.193A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.710A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 265 through 274 removed outlier: 4.197A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 77 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) removed outlier: 3.543A pdb=" N HIS E 77 " --> pdb=" O TYR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.701A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 187 No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 265 through 274 removed outlier: 3.804A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 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) removed outlier: 3.543A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.516A pdb=" N PHE F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 163 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.617A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.226A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 51 Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 153 through 163 Processing helix chain 'G' and resid 174 through 182 removed outlier: 3.568A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.809A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.634A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 Processing helix chain 'G' and resid 265 through 274 removed outlier: 4.119A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 52 Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 153 through 163 Processing helix chain 'H' and resid 174 through 182 removed outlier: 3.564A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 187 No H-bonds generated for 'chain 'H' and resid 184 through 187' Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 265 through 274 removed outlier: 4.086A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 37 through 51 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 4.288A pdb=" N ALA I 155 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 3.725A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.582A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 Processing helix chain 'I' and resid 241 through 257 Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.961A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 28 Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 112 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.622A pdb=" N ALA J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP J 163 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 3.545A pdb=" N LYS J 181 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.594A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 Processing helix chain 'J' and resid 241 through 258 Processing helix chain 'J' and resid 265 through 274 removed outlier: 4.268A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 28 Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 66 through 76 Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 174 through 181 Processing helix chain 'K' and resid 184 through 187 No H-bonds generated for 'chain 'K' and resid 184 through 187' Processing helix chain 'K' and resid 201 through 214 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 274 removed outlier: 3.781A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 28 Processing helix chain 'L' and resid 37 through 52 Processing helix chain 'L' and resid 66 through 76 Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 163 removed outlier: 4.328A pdb=" N ALA L 155 " --> pdb=" O PRO L 151 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 removed outlier: 3.774A pdb=" N ARG L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.543A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 3.894A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 257 Processing helix chain 'L' and resid 265 through 274 removed outlier: 3.971A pdb=" N GLU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 Processing helix chain 'M' and resid 37 through 51 Processing helix chain 'M' and resid 66 through 76 Processing helix chain 'M' and resid 102 through 112 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 146 through 148 No H-bonds generated for 'chain 'M' and resid 146 through 148' Processing helix chain 'M' and resid 151 through 163 removed outlier: 4.260A pdb=" N ALA M 155 " --> pdb=" O PRO M 151 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 182 removed outlier: 3.919A pdb=" N ARG M 182 " --> pdb=" O ALA M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 Processing helix chain 'M' and resid 201 through 214 Processing helix chain 'M' and resid 227 through 237 removed outlier: 4.002A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 257 Processing helix chain 'M' and resid 265 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 28 Processing helix chain 'N' and resid 37 through 51 Processing helix chain 'N' and resid 66 through 76 Processing helix chain 'N' and resid 102 through 112 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 153 through 163 Processing helix chain 'N' and resid 174 through 182 removed outlier: 4.107A pdb=" N ARG N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 189 Processing helix chain 'N' and resid 201 through 214 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 227 through 237 removed outlier: 4.087A pdb=" N ILE N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 258 Processing helix chain 'N' and resid 265 through 274 removed outlier: 4.403A pdb=" N GLU N 274 " --> pdb=" O GLU N 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 29 Processing helix chain 'O' and resid 37 through 52 Processing helix chain 'O' and resid 66 through 76 Processing helix chain 'O' and resid 102 through 112 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 146 through 148 No H-bonds generated for 'chain 'O' and resid 146 through 148' Processing helix chain 'O' and resid 153 through 163 Processing helix chain 'O' and resid 174 through 182 removed outlier: 3.652A pdb=" N ARG O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 189 Processing helix chain 'O' and resid 202 through 214 Processing helix chain 'O' and resid 227 through 237 Processing helix chain 'O' and resid 241 through 257 removed outlier: 3.694A pdb=" N GLU O 246 " --> pdb=" O GLY O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 274 removed outlier: 3.992A pdb=" N GLU O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 274 " --> pdb=" O GLU O 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 28 Processing helix chain 'P' and resid 37 through 52 Processing helix chain 'P' and resid 66 through 77 Processing helix chain 'P' and resid 102 through 112 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 146 through 148 No H-bonds generated for 'chain 'P' and resid 146 through 148' Processing helix chain 'P' and resid 153 through 163 Processing helix chain 'P' and resid 174 through 181 removed outlier: 3.536A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 189 Processing helix chain 'P' and resid 201 through 213 Processing helix chain 'P' and resid 229 through 237 Processing helix chain 'P' and resid 241 through 258 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 265 through 272 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 29 removed outlier: 3.533A pdb=" N ILE Q 25 " --> pdb=" O GLN Q 22 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 52 Processing helix chain 'Q' and resid 66 through 76 Processing helix chain 'Q' and resid 102 through 112 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 146 through 148 No H-bonds generated for 'chain 'Q' and resid 146 through 148' Processing helix chain 'Q' and resid 153 through 163 Processing helix chain 'Q' and resid 174 through 182 removed outlier: 3.613A pdb=" N ARG Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 189 Processing helix chain 'Q' and resid 201 through 214 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 227 through 237 removed outlier: 3.648A pdb=" N ALA Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 241 through 258 removed outlier: 4.305A pdb=" N GLU Q 246 " --> pdb=" O GLY Q 242 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG Q 258 " --> pdb=" O ARG Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 274 removed outlier: 3.845A pdb=" N GLU Q 274 " --> pdb=" O GLU Q 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 52 Processing helix chain 'R' and resid 58 through 72 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 76 through 94 removed outlier: 7.790A pdb=" N LEU R 91 " --> pdb=" O GLU R 87 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY R 93 " --> pdb=" O ASP R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 123 Processing helix chain 'R' and resid 131 through 145 Processing helix chain 'R' and resid 153 through 171 Proline residue: R 162 - end of helix removed outlier: 3.705A pdb=" N ALA R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS R 171 " --> pdb=" O GLN R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 260 Processing helix chain 'R' and resid 295 through 304 Processing helix chain 'R' and resid 314 through 330 removed outlier: 4.783A pdb=" N VAL R 319 " --> pdb=" O GLU R 316 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU R 321 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG R 322 " --> pdb=" O VAL R 319 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 4.214A pdb=" N ASP R 329 " --> pdb=" O THR R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 334 No H-bonds generated for 'chain 'R' and resid 332 through 334' Processing helix chain 'R' and resid 350 through 353 No H-bonds generated for 'chain 'R' and resid 350 through 353' Processing helix chain 'R' and resid 358 through 371 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 375 No H-bonds generated for 'chain 'R' and resid 373 through 375' Processing helix chain 'R' and resid 388 through 391 No H-bonds generated for 'chain 'R' and resid 388 through 391' Processing helix chain 'R' and resid 403 through 410 Processing helix chain 'R' and resid 420 through 422 No H-bonds generated for 'chain 'R' and resid 420 through 422' Processing helix chain 'R' and resid 436 through 439 Processing helix chain 'R' and resid 484 through 497 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) removed outlier: 4.370A pdb=" N THR R 496 " --> pdb=" O ARG R 492 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA R 497 " --> pdb=" O ARG R 493 " (cutoff:3.500A) Processing helix chain 'R' and resid 503 through 508 Processing helix chain 'R' and resid 526 through 540 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) removed outlier: 5.179A pdb=" N ASP R 540 " --> pdb=" O SER R 536 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 53 Processing helix chain 'S' and resid 58 through 72 removed outlier: 3.948A pdb=" N GLN S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU S 67 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA S 68 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA S 69 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU S 70 " --> pdb=" O ARG S 66 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS S 71 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 94 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 108 through 122 Processing helix chain 'S' and resid 131 through 145 Processing helix chain 'S' and resid 153 through 171 Proline residue: S 162 - end of helix Processing helix chain 'S' and resid 249 through 260 Processing helix chain 'S' and resid 295 through 304 Processing helix chain 'S' and resid 314 through 330 removed outlier: 4.656A pdb=" N VAL S 319 " --> pdb=" O GLU S 316 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG S 322 " --> pdb=" O VAL S 319 " (cutoff:3.500A) Proline residue: S 323 - end of helix removed outlier: 3.564A pdb=" N THR S 326 " --> pdb=" O PRO S 323 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN S 328 " --> pdb=" O LYS S 325 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP S 329 " --> pdb=" O THR S 326 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN S 330 " --> pdb=" O LEU S 327 " (cutoff:3.500A) Processing helix chain 'S' and resid 332 through 334 No H-bonds generated for 'chain 'S' and resid 332 through 334' Processing helix chain 'S' and resid 343 through 345 No H-bonds generated for 'chain 'S' and resid 343 through 345' Processing helix chain 'S' and resid 350 through 353 No H-bonds generated for 'chain 'S' and resid 350 through 353' Processing helix chain 'S' and resid 358 through 371 removed outlier: 4.081A pdb=" N GLN S 363 " --> pdb=" O ARG S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 386 through 391 removed outlier: 3.531A pdb=" N TRP S 390 " --> pdb=" O ARG S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 403 through 406 No H-bonds generated for 'chain 'S' and resid 403 through 406' Processing helix chain 'S' and resid 436 through 438 No H-bonds generated for 'chain 'S' and resid 436 through 438' Processing helix chain 'S' and resid 462 through 464 No H-bonds generated for 'chain 'S' and resid 462 through 464' Processing helix chain 'S' and resid 484 through 496 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) Processing helix chain 'S' and resid 503 through 511 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 534 Processing helix chain 'S' and resid 538 through 540 No H-bonds generated for 'chain 'S' and resid 538 through 540' Processing helix chain 'T' and resid 249 through 260 removed outlier: 3.516A pdb=" N ARG T 257 " --> pdb=" O ALA T 253 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 269 No H-bonds generated for 'chain 'T' and resid 267 through 269' Processing helix chain 'T' and resid 295 through 304 removed outlier: 3.526A pdb=" N LEU T 304 " --> pdb=" O GLY T 301 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 329 removed outlier: 3.574A pdb=" N ASP T 329 " --> pdb=" O THR T 326 " (cutoff:3.500A) Processing helix chain 'T' and resid 331 through 334 Processing helix chain 'T' and resid 358 through 370 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 386 through 393 Processing helix chain 'T' and resid 404 through 406 No H-bonds generated for 'chain 'T' and resid 404 through 406' Processing helix chain 'T' and resid 436 through 439 Processing helix chain 'T' and resid 484 through 500 removed outlier: 3.551A pdb=" N THR T 500 " --> pdb=" O THR T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 504 through 519 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) removed outlier: 4.165A pdb=" N THR T 519 " --> pdb=" O ALA T 515 " (cutoff:3.500A) Processing helix chain 'U' and resid 249 through 260 Processing helix chain 'U' and resid 296 through 304 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 324 through 328 removed outlier: 3.811A pdb=" N ASN U 328 " --> pdb=" O LYS U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 334 No H-bonds generated for 'chain 'U' and resid 332 through 334' Processing helix chain 'U' and resid 360 through 366 removed outlier: 3.617A pdb=" N LEU U 365 " --> pdb=" O LEU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 368 through 371 No H-bonds generated for 'chain 'U' and resid 368 through 371' Processing helix chain 'U' and resid 379 through 381 No H-bonds generated for 'chain 'U' and resid 379 through 381' Processing helix chain 'U' and resid 386 through 392 removed outlier: 3.689A pdb=" N TRP U 390 " --> pdb=" O ARG U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 403 through 409 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) No H-bonds generated for 'chain 'U' and resid 403 through 409' Processing helix chain 'U' and resid 420 through 422 No H-bonds generated for 'chain 'U' and resid 420 through 422' Processing helix chain 'U' and resid 436 through 439 Processing helix chain 'U' and resid 484 through 500 removed outlier: 3.539A pdb=" N LEU U 494 " --> pdb=" O ALA U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 503 through 505 No H-bonds generated for 'chain 'U' and resid 503 through 505' Processing helix chain 'U' and resid 507 through 519 removed outlier: 3.806A pdb=" N VAL U 511 " --> pdb=" O GLN U 508 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG U 513 " --> pdb=" O VAL U 510 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP U 514 " --> pdb=" O VAL U 511 " (cutoff:3.500A) Processing helix chain 'r' and resid 575 through 582 removed outlier: 3.617A pdb=" N ARG r 579 " --> pdb=" O TYR r 575 " (cutoff:3.500A) Processing helix chain 's' and resid 575 through 582 Processing helix chain 't' and resid 575 through 582 Processing helix chain 'u' and resid 575 through 581 Processing sheet with id= A, first strand: chain 'A' and resid 314 through 316 removed outlier: 4.502A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 607 through 611 removed outlier: 3.720A pdb=" N SER A 542 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP A 465 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL A 471 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 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= E, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.771A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 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= G, first strand: chain 'G' and resid 193 through 196 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= H, first strand: chain 'H' and resid 193 through 196 removed outlier: 6.741A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 195 removed outlier: 6.660A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 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= K, first strand: chain 'K' and resid 193 through 196 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= L, first strand: chain 'L' and resid 193 through 196 removed outlier: 6.772A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 193 through 196 removed outlier: 6.652A pdb=" N ARG M 57 " --> pdb=" O LEU M 194 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE M 196 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL M 59 " --> pdb=" O PHE M 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 193 through 196 removed outlier: 6.913A pdb=" N ARG N 57 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE N 196 " --> pdb=" O ARG N 57 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL N 59 " --> pdb=" O PHE N 196 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 193 through 195 removed outlier: 6.743A pdb=" N ARG O 57 " --> pdb=" O LEU O 194 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 193 through 196 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= Q, first strand: chain 'Q' and resid 193 through 195 removed outlier: 7.052A pdb=" N ARG Q 57 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 184 through 186 Processing sheet with id= S, first strand: chain 'R' and resid 307 through 310 removed outlier: 6.572A pdb=" N TRP R 202 " --> pdb=" O TYR R 285 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP R 231 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE R 237 " --> pdb=" O ASP R 231 " (cutoff:3.500A) Processing sheet with id= T, 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: 3.763A pdb=" N THR R 470 " --> pdb=" O VAL R 458 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG R 460 " --> pdb=" O PHE R 468 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE R 468 " --> pdb=" O ARG R 460 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU R 462 " --> pdb=" O GLU R 466 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU R 466 " --> pdb=" O GLU R 462 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'R' and resid 424 through 426 removed outlier: 3.602A pdb=" N LEU R 424 " --> pdb=" O TYR R 431 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU R 429 " --> pdb=" O PHE R 426 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S' and resid 184 through 186 Processing sheet with id= W, first strand: chain 'S' and resid 307 through 310 removed outlier: 6.151A pdb=" N TRP S 202 " --> pdb=" O TYR S 285 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP S 205 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY S 239 " --> pdb=" O VAL S 229 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP S 231 " --> pdb=" O ILE S 237 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE S 237 " --> pdb=" O ASP S 231 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'S' and resid 411 through 413 removed outlier: 3.713A pdb=" N MET S 411 " --> pdb=" O PHE S 448 " (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: 8.522A pdb=" N THR S 454 " --> pdb=" O ALA S 474 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA S 474 " --> pdb=" O THR S 454 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR S 470 " --> pdb=" O VAL S 458 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG S 460 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE S 468 " --> pdb=" O ARG S 460 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 416 through 418 removed outlier: 3.697A pdb=" N ARG S 416 " --> pdb=" O VAL S 444 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'T' and resid 283 through 285 removed outlier: 6.751A pdb=" N ASP T 231 " --> pdb=" O ILE T 237 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE T 237 " --> pdb=" O ASP T 231 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'T' and resid 423 through 426 removed outlier: 4.693A pdb=" N MET T 430 " --> pdb=" O GLN T 475 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL T 458 " --> pdb=" O LEU T 469 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG T 471 " --> pdb=" O ILE T 456 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE T 456 " --> pdb=" O ARG T 471 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'U' and resid 240 through 243 removed outlier: 6.624A pdb=" N HIS U 283 " --> pdb=" O TRP U 202 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS U 204 " --> pdb=" O HIS U 283 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR U 285 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N HIS U 206 " --> pdb=" O TYR U 285 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL U 307 " --> pdb=" O PHE U 284 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR U 286 " --> pdb=" O VAL U 307 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS U 309 " --> pdb=" O THR U 286 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'U' and resid 424 through 426 Processing sheet with id= AD, first strand: chain 'U' and resid 445 through 448 removed outlier: 6.235A pdb=" N ARG U 460 " --> pdb=" O PHE U 468 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE U 468 " --> pdb=" O ARG U 460 " (cutoff:3.500A) 2152 hydrogen bonds defined for protein. 6186 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: 24.57 Time building geometry restraints manager: 24.72 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: 96.01 - 104.83: 2721 104.83 - 113.65: 36814 113.65 - 122.46: 38535 122.46 - 131.28: 8612 131.28 - 140.10: 304 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: 187 2.37 - 3.00: 32528 3.00 - 3.64: 98798 3.64 - 4.27: 160539 4.27 - 4.90: 245636 Nonbonded interactions: 537688 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 537683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.320 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: 0.060 Extract box with map and model: 7.260 Check model and map are aligned: 0.380 Set scattering table: 0.440 Process input model: 155.190 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.460 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.320 ------------------------------------------------------------------------------- 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= 0.363 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 : 4.831 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: 1.7469 time to fit residues: 2070.6202 Evaluate side-chains 710 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 696 time to evaluate : 4.756 ------------------------------------------------------------------------------- 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: 5.9990 chunk 488 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 504 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 chunk 584 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 521 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 135 ASN C 137 GLN G 206 ASN H 38 GLN H 213 GLN K 206 ASN N 81 GLN N 213 GLN P 77 HIS Q 81 GLN R 217 HIS R 425 GLN ** R 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1346 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= 0.241 Angle : 0.637 10.042 86986 Z= 0.350 Chirality : 0.043 0.321 9900 Planarity : 0.005 0.077 9171 Dihedral : 21.848 178.981 14248 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.01 % Allowed : 10.75 % Favored : 87.24 % 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: 0.49 (0.09), residues: 3292 sheet: -0.08 (0.21), residues: 491 loop : 0.38 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 86 HIS 0.007 0.001 HIS P 77 PHE 0.019 0.002 PHE S 306 TYR 0.020 0.002 TYR u 582 ARG 0.008 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 819 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 712 time to evaluate : 4.912 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: 0.7702 (tmm160) cc_final: 0.6791 (mpt180) REVERT: A 362 LYS cc_start: 0.7685 (mptt) cc_final: 0.7399 (mmtt) REVERT: A 416 GLN cc_start: 0.7799 (tp40) cc_final: 0.7539 (tp-100) REVERT: A 456 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 492 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7415 (ttp80) REVERT: A 539 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8452 (mppt) REVERT: A 566 LYS cc_start: 0.8015 (tttp) cc_final: 0.7750 (ttmp) REVERT: B 9 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6936 (ttmt) REVERT: B 27 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: D 107 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7500 (ttpp) REVERT: D 227 LYS cc_start: 0.6649 (mttp) cc_final: 0.6324 (mptm) REVERT: E 131 GLU cc_start: 0.8088 (tp30) cc_final: 0.7812 (mm-30) REVERT: E 231 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7441 (tpp-160) REVERT: E 270 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6920 (mp0) REVERT: F 131 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7592 (mm-30) REVERT: F 209 GLU cc_start: 0.8068 (tt0) cc_final: 0.7759 (tp30) REVERT: G 225 LYS cc_start: 0.7509 (pmmt) cc_final: 0.7278 (ptpp) REVERT: G 269 GLN cc_start: 0.7418 (mm110) cc_final: 0.7015 (mt0) REVERT: G 273 LYS cc_start: 0.8319 (ptmm) cc_final: 0.8020 (pttp) REVERT: G 275 TYR cc_start: 0.6800 (m-80) cc_final: 0.6581 (m-80) REVERT: H 209 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: H 261 LYS cc_start: 0.7980 (mptt) cc_final: 0.7406 (mptm) REVERT: I 78 LYS cc_start: 0.7246 (pmmt) cc_final: 0.6918 (pmtt) REVERT: I 114 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7849 (mtpp) REVERT: J 196 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8246 (t80) REVERT: K 22 GLN cc_start: 0.7787 (mp10) cc_final: 0.7360 (mm-40) REVERT: K 175 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8032 (ttp80) REVERT: L 76 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7382 (mtp180) REVERT: L 246 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7177 (mp0) REVERT: M 175 ARG cc_start: 0.7420 (tpt-90) cc_final: 0.7166 (tpt170) REVERT: M 184 GLU cc_start: 0.7865 (tt0) cc_final: 0.7471 (pm20) REVERT: M 205 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7458 (mttt) REVERT: N 246 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6347 (mm-30) REVERT: O 238 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: O 265 LYS cc_start: 0.6641 (ttmt) cc_final: 0.6425 (tmtt) REVERT: O 269 GLN cc_start: 0.7360 (tp40) cc_final: 0.7120 (tp40) REVERT: O 273 LYS cc_start: 0.8553 (ttpt) cc_final: 0.7654 (ttmt) REVERT: P 182 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6807 (mtp180) REVERT: P 209 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: P 249 ARG cc_start: 0.6685 (mtt-85) cc_final: 0.6401 (mpt-90) REVERT: Q 63 ARG cc_start: 0.6240 (mmt90) cc_final: 0.5572 (mmp-170) REVERT: Q 128 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6397 (tpt170) REVERT: Q 214 MET cc_start: 0.4779 (mpt) cc_final: 0.4409 (mpp) REVERT: Q 229 MET cc_start: 0.3190 (mpt) cc_final: 0.1899 (tpp) REVERT: R 165 GLU cc_start: 0.8546 (tp30) cc_final: 0.8278 (tp30) REVERT: R 172 SER cc_start: 0.7206 (t) cc_final: 0.6781 (p) REVERT: R 188 ARG cc_start: 0.7498 (ttm170) cc_final: 0.6731 (tmm160) REVERT: R 345 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7498 (mm-30) REVERT: R 381 MET cc_start: 0.8621 (mmm) cc_final: 0.8258 (mmm) REVERT: S 268 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: S 378 ASP cc_start: 0.8194 (t0) cc_final: 0.7299 (m-30) REVERT: S 430 MET cc_start: 0.8072 (mtp) cc_final: 0.7823 (mpp) REVERT: T 199 ASN cc_start: 0.4594 (OUTLIER) cc_final: 0.4213 (t0) REVERT: T 202 TRP cc_start: 0.6030 (m-10) cc_final: 0.5802 (m-10) REVERT: T 235 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7268 (mpp-170) REVERT: T 268 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: T 327 LEU cc_start: 0.6306 (mm) cc_final: 0.5938 (mm) REVERT: T 373 TYR cc_start: 0.5114 (OUTLIER) cc_final: 0.4023 (t80) REVERT: T 381 MET cc_start: 0.4844 (tpt) cc_final: 0.4522 (tpt) REVERT: U 238 MET cc_start: 0.2757 (ptm) cc_final: 0.2103 (pmm) REVERT: U 245 ASP cc_start: 0.7005 (t0) cc_final: 0.6583 (t0) REVERT: U 412 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7250 (tptt) REVERT: U 434 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: U 473 HIS cc_start: 0.6503 (OUTLIER) cc_final: 0.5866 (m90) REVERT: s 575 TYR cc_start: 0.3493 (OUTLIER) cc_final: 0.2330 (t80) REVERT: t 575 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3411 (m-80) outliers start: 107 outliers final: 29 residues processed: 765 average time/residue: 1.7454 time to fit residues: 1635.7864 Evaluate side-chains 697 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 649 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET 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 E residue 196 PHE Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER 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 I residue 256 LEU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 238 GLU 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 228 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 495 ARG Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 412 LYS Chi-restraints excluded: chain U residue 417 THR Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 453 ILE 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: 0.9990 chunk 181 optimal weight: 9.9990 chunk 486 optimal weight: 20.0000 chunk 398 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 585 optimal weight: 20.0000 chunk 632 optimal weight: 9.9990 chunk 521 optimal weight: 7.9990 chunk 580 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 470 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 C 33 ASN D 77 HIS F 213 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN L 185 GLN N 213 GLN Q 81 GLN R 427 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7526 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 62692 Z= 0.322 Angle : 0.648 13.585 86986 Z= 0.351 Chirality : 0.044 0.336 9900 Planarity : 0.005 0.070 9171 Dihedral : 21.905 178.276 14228 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.42 % Allowed : 12.53 % Favored : 85.04 % 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: 0.53 (0.11), residues: 6033 helix: 0.63 (0.09), residues: 3309 sheet: -0.09 (0.22), residues: 470 loop : 0.28 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 225 HIS 0.009 0.001 HIS S 473 PHE 0.027 0.002 PHE S 306 TYR 0.024 0.002 TYR R 233 ARG 0.007 0.001 ARG R 235 *********************** 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 818 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 689 time to evaluate : 4.864 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: 0.7735 (tmm160) cc_final: 0.6886 (mpt180) REVERT: A 362 LYS cc_start: 0.7806 (mptt) cc_final: 0.7548 (mmtt) REVERT: A 416 GLN cc_start: 0.7820 (tp40) cc_final: 0.7503 (tp-100) REVERT: A 456 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: A 492 ARG cc_start: 0.8269 (ttp-110) cc_final: 0.7365 (ttp80) REVERT: A 539 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8445 (mppt) REVERT: A 566 LYS cc_start: 0.8058 (tttp) cc_final: 0.7779 (ttmp) REVERT: D 107 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7509 (ttpp) REVERT: E 76 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6569 (ttp-170) REVERT: E 131 GLU cc_start: 0.8101 (tp30) cc_final: 0.7844 (mm-30) REVERT: E 231 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7382 (tpp-160) REVERT: E 270 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6974 (mp0) REVERT: F 209 GLU cc_start: 0.8072 (tt0) cc_final: 0.7847 (tp30) REVERT: F 213 GLN cc_start: 0.7735 (mt0) cc_final: 0.7408 (mt0) REVERT: F 273 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7830 (mtpt) REVERT: G 225 LYS cc_start: 0.7526 (pmmt) cc_final: 0.7220 (ptpp) REVERT: G 269 GLN cc_start: 0.7520 (mm110) cc_final: 0.7089 (mt0) REVERT: H 261 LYS cc_start: 0.8049 (mptt) cc_final: 0.7452 (mptm) REVERT: I 114 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7838 (mtpp) REVERT: J 78 LYS cc_start: 0.7681 (mmmm) cc_final: 0.7353 (mmmt) REVERT: J 196 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8158 (t80) REVERT: K 149 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8316 (mp) REVERT: K 175 ARG cc_start: 0.8398 (ttm170) cc_final: 0.8057 (ttt90) REVERT: K 196 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8817 (t80) REVERT: L 76 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: L 225 LYS cc_start: 0.8012 (pptt) cc_final: 0.7638 (ptmm) REVERT: L 246 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7152 (mp0) REVERT: M 175 ARG cc_start: 0.7415 (tpt-90) cc_final: 0.7167 (tpt170) REVERT: M 184 GLU cc_start: 0.7989 (tt0) cc_final: 0.7543 (pm20) REVERT: M 205 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7447 (mttt) REVERT: M 209 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: M 211 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.7086 (t-100) REVERT: O 269 GLN cc_start: 0.7348 (tp40) cc_final: 0.7138 (tp40) REVERT: P 182 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6901 (mtp180) REVERT: Q 63 ARG cc_start: 0.6242 (mmt90) cc_final: 0.5574 (mmp-170) REVERT: Q 128 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6418 (tpt170) REVERT: Q 214 MET cc_start: 0.4784 (mpt) cc_final: 0.4529 (mpp) REVERT: Q 229 MET cc_start: 0.3088 (mpt) cc_final: 0.1818 (tpp) REVERT: Q 250 GLU cc_start: 0.5258 (tp30) cc_final: 0.3919 (pt0) REVERT: R 104 LYS cc_start: 0.7565 (mttt) cc_final: 0.6747 (ttmm) REVERT: R 165 GLU cc_start: 0.8570 (tp30) cc_final: 0.8254 (tp30) REVERT: R 188 ARG cc_start: 0.7534 (ttm170) cc_final: 0.6760 (tmm160) REVERT: R 215 ASP cc_start: 0.7194 (t0) cc_final: 0.6968 (t70) REVERT: R 465 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8189 (mm-40) REVERT: S 76 LEU cc_start: 0.7290 (pt) cc_final: 0.6762 (tt) REVERT: S 165 GLU cc_start: 0.8247 (pt0) cc_final: 0.7981 (mm-30) REVERT: S 268 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8193 (pp20) REVERT: S 299 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6121 (mt0) REVERT: S 384 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: T 199 ASN cc_start: 0.4560 (OUTLIER) cc_final: 0.4321 (t0) REVERT: T 268 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: T 327 LEU cc_start: 0.6255 (mm) cc_final: 0.5839 (mm) REVERT: T 373 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.4274 (t80) REVERT: T 488 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: U 238 MET cc_start: 0.2553 (ptm) cc_final: 0.1880 (pmm) REVERT: U 245 ASP cc_start: 0.7105 (t0) cc_final: 0.6640 (t0) REVERT: U 300 ILE cc_start: 0.8622 (pp) cc_final: 0.8347 (mp) REVERT: U 404 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.4578 (mmp-170) REVERT: U 412 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7390 (tptt) REVERT: U 434 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: U 473 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.5973 (m90) REVERT: r 575 TYR cc_start: 0.2926 (OUTLIER) cc_final: 0.2190 (m-80) REVERT: s 575 TYR cc_start: 0.3538 (OUTLIER) cc_final: 0.2749 (t80) REVERT: t 575 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.3413 (m-80) outliers start: 129 outliers final: 47 residues processed: 769 average time/residue: 1.7317 time to fit residues: 1634.7561 Evaluate side-chains 703 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 630 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET 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 D residue 62 SER Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 273 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 256 LEU 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 210 MET Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 261 LYS 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 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 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 206 HIS Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR 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 384 GLN Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 488 GLU Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 412 LYS Chi-restraints excluded: chain U residue 417 THR Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 470 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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 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: 8.9990 chunk 304 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 393 optimal weight: 5.9990 chunk 587 optimal weight: 10.0000 chunk 622 optimal weight: 0.1980 chunk 307 optimal weight: 6.9990 chunk 557 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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 ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 62692 Z= 0.261 Angle : 0.605 15.558 86986 Z= 0.327 Chirality : 0.042 0.315 9900 Planarity : 0.005 0.066 9171 Dihedral : 21.885 178.568 14224 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 13.27 % Favored : 83.78 % 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: 0.65 (0.11), residues: 6033 helix: 0.80 (0.09), residues: 3306 sheet: -0.14 (0.22), residues: 472 loop : 0.23 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP U 225 HIS 0.006 0.001 HIS L 77 PHE 0.020 0.002 PHE S 306 TYR 0.021 0.002 TYR R 233 ARG 0.012 0.000 ARG R 235 *********************** 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 824 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 667 time to evaluate : 4.900 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: 0.8379 (OUTLIER) cc_final: 0.8111 (ttmm) REVERT: A 275 ARG cc_start: 0.7747 (tmm160) cc_final: 0.6886 (mpt180) REVERT: A 362 LYS cc_start: 0.7858 (mptt) cc_final: 0.7600 (mmtt) REVERT: A 416 GLN cc_start: 0.7816 (tp40) cc_final: 0.7506 (tp-100) REVERT: A 456 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: A 492 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7357 (ttp80) REVERT: A 539 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8434 (mppt) REVERT: A 566 LYS cc_start: 0.8035 (tttp) cc_final: 0.7738 (ttmp) REVERT: B 49 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.7750 (tmtt) REVERT: C 156 MET cc_start: 0.9057 (ttm) cc_final: 0.8760 (ttm) REVERT: D 107 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7469 (ttpp) REVERT: E 76 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6571 (ttp-170) REVERT: E 131 GLU cc_start: 0.8109 (tp30) cc_final: 0.7865 (mm-30) REVERT: E 231 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7902 (ttp80) REVERT: E 270 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6935 (mp0) REVERT: F 74 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7546 (ppt-90) REVERT: F 209 GLU cc_start: 0.8072 (tt0) cc_final: 0.7742 (tm-30) REVERT: F 273 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7847 (mtpt) REVERT: G 225 LYS cc_start: 0.7420 (pmmt) cc_final: 0.7136 (ptpp) REVERT: G 269 GLN cc_start: 0.7570 (mm110) cc_final: 0.7089 (mt0) REVERT: H 261 LYS cc_start: 0.8068 (mptt) cc_final: 0.7464 (mptm) REVERT: I 114 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7815 (mtpp) REVERT: J 78 LYS cc_start: 0.7726 (mmmm) cc_final: 0.7403 (mmmt) REVERT: J 196 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8118 (t80) REVERT: K 149 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8125 (mp) REVERT: K 175 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8037 (ttt90) REVERT: K 196 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8820 (t80) REVERT: L 76 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7478 (mtp180) REVERT: L 225 LYS cc_start: 0.8013 (pptt) cc_final: 0.7638 (ptmm) REVERT: L 246 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6930 (mp0) REVERT: M 175 ARG cc_start: 0.7381 (tpt-90) cc_final: 0.7118 (tpt90) REVERT: M 184 GLU cc_start: 0.7974 (tt0) cc_final: 0.7556 (pm20) REVERT: M 205 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7452 (mttt) REVERT: M 209 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: M 211 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7101 (t-100) REVERT: M 223 ASN cc_start: 0.5836 (OUTLIER) cc_final: 0.5508 (m110) REVERT: M 273 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7823 (tptt) REVERT: O 210 MET cc_start: 0.7051 (mtp) cc_final: 0.6695 (mtt) REVERT: O 214 MET cc_start: 0.6413 (mpp) cc_final: 0.6207 (pmm) REVERT: O 269 GLN cc_start: 0.7368 (tp40) cc_final: 0.7149 (tp40) REVERT: P 182 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6907 (mtp180) REVERT: Q 63 ARG cc_start: 0.6234 (mmt90) cc_final: 0.5540 (mmp-170) REVERT: Q 214 MET cc_start: 0.4850 (mpt) cc_final: 0.4629 (mpp) REVERT: Q 229 MET cc_start: 0.3081 (mpt) cc_final: 0.1845 (tpp) REVERT: Q 250 GLU cc_start: 0.5215 (tp30) cc_final: 0.3924 (pt0) REVERT: R 104 LYS cc_start: 0.7597 (mttt) cc_final: 0.6770 (ttmm) REVERT: R 165 GLU cc_start: 0.8555 (tp30) cc_final: 0.8309 (tp30) REVERT: R 188 ARG cc_start: 0.7518 (ttm170) cc_final: 0.6727 (tmm160) REVERT: R 381 MET cc_start: 0.8536 (mmm) cc_final: 0.8240 (mmm) REVERT: R 465 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8164 (mm-40) REVERT: S 76 LEU cc_start: 0.7223 (pt) cc_final: 0.6719 (tt) REVERT: S 268 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8201 (pp20) REVERT: S 295 ASN cc_start: 0.7919 (m-40) cc_final: 0.7413 (m-40) REVERT: S 299 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.5989 (mt0) REVERT: S 349 ASP cc_start: 0.6588 (t70) cc_final: 0.6324 (t0) REVERT: S 384 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: S 471 ARG cc_start: 0.6527 (ptm-80) cc_final: 0.5541 (tmt-80) REVERT: T 268 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: T 325 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8095 (pmmt) REVERT: T 327 LEU cc_start: 0.6298 (mm) cc_final: 0.5887 (mm) REVERT: T 338 TYR cc_start: 0.6881 (p90) cc_final: 0.6355 (p90) REVERT: T 373 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.4285 (t80) REVERT: T 411 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6872 (mtm) REVERT: T 434 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: U 238 MET cc_start: 0.2633 (ptm) cc_final: 0.1819 (pmm) REVERT: U 245 ASP cc_start: 0.7184 (t0) cc_final: 0.6570 (t0) REVERT: U 300 ILE cc_start: 0.8653 (pp) cc_final: 0.8356 (mp) REVERT: U 324 PHE cc_start: 0.7780 (p90) cc_final: 0.7441 (p90) REVERT: U 372 ARG cc_start: 0.6367 (ttp80) cc_final: 0.5654 (ttp-110) REVERT: U 412 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7313 (tptt) REVERT: U 434 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: U 473 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.5959 (m90) REVERT: r 575 TYR cc_start: 0.2851 (OUTLIER) cc_final: 0.2144 (m-80) REVERT: s 578 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.2217 (tp) REVERT: t 575 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.3442 (m-80) outliers start: 157 outliers final: 59 residues processed: 764 average time/residue: 1.7160 time to fit residues: 1611.8705 Evaluate side-chains 720 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 632 time to evaluate : 4.834 ------------------------------------------------------------------------------- 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 B residue 76 ARG 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 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 196 PHE 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 F residue 273 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 264 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 256 LEU 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 M residue 180 ILE Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 211 TRP 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 180 ILE Chi-restraints excluded: chain P residue 64 THR 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 218 LEU Chi-restraints excluded: chain R residue 46 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 236 CYS Chi-restraints excluded: chain R residue 319 VAL 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 33 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 123 ASN Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 268 GLU 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 384 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 T residue 268 GLU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 411 MET Chi-restraints excluded: chain T residue 434 GLU Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 412 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 485 ASP 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 578 LEU 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: 2.9990 chunk 353 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 463 optimal weight: 3.9990 chunk 256 optimal weight: 0.0980 chunk 531 optimal weight: 8.9990 chunk 430 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 558 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 415 GLN A 442 GLN C 33 ASN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN M 80 GLN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 427 GLN S 461 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 295 ASN ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 62692 Z= 0.207 Angle : 0.569 11.654 86986 Z= 0.308 Chirality : 0.040 0.296 9900 Planarity : 0.004 0.064 9171 Dihedral : 21.829 179.624 14224 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 14.54 % Favored : 82.68 % 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: 0.87 (0.11), residues: 6033 helix: 1.01 (0.09), residues: 3304 sheet: -0.13 (0.22), residues: 472 loop : 0.30 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 225 HIS 0.006 0.001 HIS R 283 PHE 0.016 0.001 PHE S 306 TYR 0.021 0.001 TYR R 435 ARG 0.008 0.000 ARG U 493 *********************** 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 820 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 672 time to evaluate : 4.906 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: 0.7711 (tmm160) cc_final: 0.6861 (mpt180) REVERT: A 362 LYS cc_start: 0.7827 (mptt) cc_final: 0.7613 (mmtt) REVERT: A 416 GLN cc_start: 0.7800 (tp40) cc_final: 0.7500 (tp-100) REVERT: A 492 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7343 (ttp80) REVERT: A 539 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8418 (mppt) REVERT: A 566 LYS cc_start: 0.8008 (tttp) cc_final: 0.7702 (ttmp) REVERT: B 20 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: B 49 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.7782 (tmtt) REVERT: C 156 MET cc_start: 0.8994 (ttm) cc_final: 0.8735 (ttt) REVERT: D 107 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7473 (ttpp) REVERT: E 76 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6402 (ttp-170) REVERT: E 131 GLU cc_start: 0.8093 (tp30) cc_final: 0.7865 (mm-30) REVERT: E 231 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7855 (ttp80) REVERT: E 270 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6917 (mp0) REVERT: F 209 GLU cc_start: 0.8047 (tt0) cc_final: 0.7756 (tm-30) REVERT: G 269 GLN cc_start: 0.7595 (mm110) cc_final: 0.7098 (mt0) REVERT: H 261 LYS cc_start: 0.8079 (mptt) cc_final: 0.7468 (mptm) REVERT: I 114 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7781 (mtpp) REVERT: J 78 LYS cc_start: 0.7713 (mmmm) cc_final: 0.7388 (mmmt) REVERT: J 196 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8181 (t80) REVERT: K 61 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7617 (mp0) REVERT: K 149 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8075 (mp) REVERT: K 175 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8080 (ttp80) REVERT: K 196 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8657 (t80) REVERT: K 225 LYS cc_start: 0.7540 (ttpm) cc_final: 0.7310 (ttmt) REVERT: L 225 LYS cc_start: 0.8051 (pptt) cc_final: 0.7685 (ptmm) REVERT: L 246 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6931 (mp0) REVERT: M 21 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7096 (tp) REVERT: M 175 ARG cc_start: 0.7360 (tpt-90) cc_final: 0.7126 (tpt170) REVERT: M 184 GLU cc_start: 0.7925 (tt0) cc_final: 0.7535 (pm20) REVERT: M 205 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7445 (mttt) REVERT: M 211 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.7012 (t-100) REVERT: M 223 ASN cc_start: 0.5807 (OUTLIER) cc_final: 0.5481 (m110) REVERT: M 273 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7817 (tptt) REVERT: N 210 MET cc_start: 0.6825 (mtp) cc_final: 0.6615 (mtp) REVERT: O 210 MET cc_start: 0.7076 (mtp) cc_final: 0.6695 (mtt) REVERT: O 269 GLN cc_start: 0.7413 (tp40) cc_final: 0.7180 (tp40) REVERT: O 273 LYS cc_start: 0.8476 (ttpt) cc_final: 0.7920 (tttp) REVERT: P 131 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: P 181 LYS cc_start: 0.7716 (ptmm) cc_final: 0.6784 (pttt) REVERT: P 182 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6941 (mtp180) REVERT: Q 128 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6342 (tpt170) REVERT: Q 229 MET cc_start: 0.3097 (mpt) cc_final: 0.1878 (tpp) REVERT: R 104 LYS cc_start: 0.7597 (mttt) cc_final: 0.6738 (ttmm) REVERT: R 165 GLU cc_start: 0.8627 (tp30) cc_final: 0.8375 (tp30) REVERT: R 188 ARG cc_start: 0.7534 (ttm170) cc_final: 0.6742 (tmm160) REVERT: R 191 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7580 (tptp) REVERT: R 381 MET cc_start: 0.8560 (mmm) cc_final: 0.8269 (mmm) REVERT: R 480 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: S 76 LEU cc_start: 0.7205 (pt) cc_final: 0.6704 (tt) REVERT: S 268 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: S 295 ASN cc_start: 0.7857 (m-40) cc_final: 0.7400 (m-40) REVERT: S 299 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6025 (mt0) REVERT: S 349 ASP cc_start: 0.6669 (t70) cc_final: 0.6376 (t0) REVERT: S 384 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: S 427 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5325 (mp-120) REVERT: S 471 ARG cc_start: 0.6346 (ptm-80) cc_final: 0.5438 (tmt-80) REVERT: T 268 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: T 325 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (pmmt) REVERT: T 327 LEU cc_start: 0.6266 (mm) cc_final: 0.5848 (mm) REVERT: T 338 TYR cc_start: 0.6947 (p90) cc_final: 0.6427 (p90) REVERT: T 373 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.4594 (t80) REVERT: T 488 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: U 201 VAL cc_start: 0.5425 (OUTLIER) cc_final: 0.5129 (t) REVERT: U 225 TRP cc_start: 0.6259 (OUTLIER) cc_final: 0.5937 (m-10) REVERT: U 238 MET cc_start: 0.2668 (ptm) cc_final: 0.1940 (pmm) REVERT: U 241 ASN cc_start: 0.5753 (OUTLIER) cc_final: 0.5410 (m-40) REVERT: U 372 ARG cc_start: 0.6324 (ttp80) cc_final: 0.5658 (ttp-110) REVERT: U 404 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5431 (mmp-170) REVERT: U 412 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7295 (tptt) REVERT: U 434 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: U 473 HIS cc_start: 0.6560 (OUTLIER) cc_final: 0.5940 (m90) REVERT: r 575 TYR cc_start: 0.2843 (OUTLIER) cc_final: 0.2177 (m-80) REVERT: s 575 TYR cc_start: 0.3527 (OUTLIER) cc_final: 0.3195 (t80) REVERT: s 578 LEU cc_start: 0.2461 (OUTLIER) cc_final: 0.2115 (tp) REVERT: t 575 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.3493 (m-80) outliers start: 148 outliers final: 55 residues processed: 761 average time/residue: 1.7103 time to fit residues: 1602.2958 Evaluate side-chains 721 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 633 time to evaluate : 4.863 ------------------------------------------------------------------------------- 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 B residue 76 ARG Chi-restraints excluded: chain D residue 62 SER 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 E residue 76 ARG Chi-restraints excluded: chain F residue 261 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER 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 I residue 256 LEU 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 M residue 21 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP 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 P residue 117 VAL Chi-restraints excluded: chain P residue 131 GLU 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 68 VAL Chi-restraints excluded: chain Q residue 128 ARG Chi-restraints excluded: chain Q residue 183 ASP Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU 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 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 S residue 74 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR 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 384 GLN Chi-restraints excluded: chain S residue 410 LEU Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 488 GLU Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 241 ASN Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 412 LYS Chi-restraints excluded: chain U residue 417 THR 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 485 ASP 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 s residue 578 LEU Chi-restraints excluded: chain t residue 575 TYR Chi-restraints excluded: chain u residue 580 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 8.9990 chunk 560 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 365 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 623 optimal weight: 1.9990 chunk 517 optimal weight: 0.0470 chunk 288 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 overall best weight: 1.8482 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN R 37 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 62692 Z= 0.163 Angle : 0.543 11.775 86986 Z= 0.293 Chirality : 0.039 0.276 9900 Planarity : 0.004 0.063 9171 Dihedral : 21.747 179.272 14224 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.46 % Allowed : 15.30 % Favored : 82.24 % 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: 1.09 (0.11), residues: 6033 helix: 1.22 (0.09), residues: 3308 sheet: -0.09 (0.22), residues: 516 loop : 0.37 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 225 HIS 0.006 0.001 HIS R 283 PHE 0.014 0.001 PHE S 306 TYR 0.019 0.001 TYR R 435 ARG 0.009 0.000 ARG U 493 *********************** 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 789 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 658 time to evaluate : 5.083 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: 0.7694 (tmm160) cc_final: 0.6833 (mpt180) REVERT: A 362 LYS cc_start: 0.7817 (mptt) cc_final: 0.7607 (mmtt) REVERT: A 416 GLN cc_start: 0.7772 (tp40) cc_final: 0.7499 (tp-100) REVERT: A 456 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: A 486 GLU cc_start: 0.7829 (pm20) cc_final: 0.7546 (pm20) REVERT: A 492 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7334 (ttp80) REVERT: A 539 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8423 (mppt) REVERT: A 551 MET cc_start: 0.8156 (mmm) cc_final: 0.7917 (mmm) REVERT: B 20 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: B 49 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7778 (tmtt) REVERT: C 156 MET cc_start: 0.8927 (ttm) cc_final: 0.8620 (ttt) REVERT: D 107 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7458 (ttpp) REVERT: E 38 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: E 76 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6484 (ttp-170) REVERT: E 131 GLU cc_start: 0.8104 (tp30) cc_final: 0.7879 (mm-30) REVERT: E 225 LYS cc_start: 0.6796 (tptp) cc_final: 0.6473 (tmmt) REVERT: E 231 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7767 (ttp80) REVERT: E 270 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6862 (mp0) REVERT: F 74 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7429 (ppt-90) REVERT: G 269 GLN cc_start: 0.7591 (mm110) cc_final: 0.7101 (mt0) REVERT: H 261 LYS cc_start: 0.8067 (mptt) cc_final: 0.7478 (mptm) REVERT: I 78 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6931 (pmtt) REVERT: I 114 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: J 78 LYS cc_start: 0.7674 (mmmm) cc_final: 0.7419 (mmmt) REVERT: J 196 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8161 (t80) REVERT: J 206 ASN cc_start: 0.8050 (m-40) cc_final: 0.7658 (m110) REVERT: K 61 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7592 (mp0) REVERT: K 99 LYS cc_start: 0.8912 (mttp) cc_final: 0.8224 (mmpt) REVERT: K 175 ARG cc_start: 0.8332 (ttm170) cc_final: 0.8062 (ttp80) REVERT: K 196 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8632 (t80) REVERT: K 225 LYS cc_start: 0.7485 (ttpm) cc_final: 0.7284 (ttmt) REVERT: L 21 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6898 (tm) REVERT: L 225 LYS cc_start: 0.8054 (pptt) cc_final: 0.7757 (ptmm) REVERT: L 246 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6833 (mp0) REVERT: M 21 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7095 (tp) REVERT: M 175 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.7152 (tpt170) REVERT: M 184 GLU cc_start: 0.7916 (tt0) cc_final: 0.7514 (pm20) REVERT: M 205 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7453 (mttt) REVERT: M 211 TRP cc_start: 0.7602 (t-100) cc_final: 0.6935 (t-100) REVERT: M 223 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5491 (m110) REVERT: M 273 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7806 (tptt) REVERT: O 210 MET cc_start: 0.7071 (mtp) cc_final: 0.6702 (mtt) REVERT: O 269 GLN cc_start: 0.7426 (tp40) cc_final: 0.7201 (tp40) REVERT: O 273 LYS cc_start: 0.8457 (ttpt) cc_final: 0.7897 (tttp) REVERT: P 181 LYS cc_start: 0.7742 (ptmm) cc_final: 0.6822 (pttt) REVERT: Q 128 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6333 (tpt170) REVERT: Q 229 MET cc_start: 0.3105 (mpt) cc_final: 0.1875 (tpp) REVERT: R 104 LYS cc_start: 0.7586 (mttt) cc_final: 0.6735 (ttmm) REVERT: R 165 GLU cc_start: 0.8624 (tp30) cc_final: 0.8414 (tp30) REVERT: R 188 ARG cc_start: 0.7528 (ttm170) cc_final: 0.6729 (tmm160) REVERT: R 191 LYS cc_start: 0.7888 (tmtt) cc_final: 0.7652 (tptp) REVERT: R 316 GLU cc_start: 0.7876 (mp0) cc_final: 0.7609 (mp0) REVERT: R 381 MET cc_start: 0.8616 (mmm) cc_final: 0.8297 (mmm) REVERT: R 480 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: S 76 LEU cc_start: 0.7184 (pt) cc_final: 0.6696 (tt) REVERT: S 268 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8157 (pp20) REVERT: S 295 ASN cc_start: 0.7775 (m-40) cc_final: 0.7353 (m-40) REVERT: S 299 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.5849 (mt0) REVERT: S 384 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: S 471 ARG cc_start: 0.6355 (ptm-80) cc_final: 0.5614 (tmt-80) REVERT: T 199 ASN cc_start: 0.5162 (t0) cc_final: 0.4898 (t0) REVERT: T 214 VAL cc_start: 0.7384 (p) cc_final: 0.7144 (p) REVERT: T 238 MET cc_start: 0.5940 (mpp) cc_final: 0.4999 (mmt) REVERT: T 268 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: T 327 LEU cc_start: 0.6199 (mm) cc_final: 0.5799 (mm) REVERT: T 355 ARG cc_start: 0.7792 (tmm160) cc_final: 0.7438 (tpt90) REVERT: T 373 TYR cc_start: 0.5358 (OUTLIER) cc_final: 0.4641 (t80) REVERT: T 405 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.5899 (m-30) REVERT: U 238 MET cc_start: 0.2686 (ptm) cc_final: 0.1991 (pmm) REVERT: U 241 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5402 (m-40) REVERT: U 372 ARG cc_start: 0.6307 (ttp80) cc_final: 0.5659 (ttp-110) REVERT: U 404 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5401 (mmp-170) REVERT: U 434 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: U 473 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.5831 (m90) REVERT: r 575 TYR cc_start: 0.2838 (OUTLIER) cc_final: 0.2162 (m-80) REVERT: s 575 TYR cc_start: 0.3548 (OUTLIER) cc_final: 0.3196 (t80) REVERT: s 578 LEU cc_start: 0.2453 (OUTLIER) cc_final: 0.2081 (tp) REVERT: t 575 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.3488 (m-80) outliers start: 131 outliers final: 50 residues processed: 748 average time/residue: 1.7184 time to fit residues: 1581.7020 Evaluate side-chains 703 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 624 time to evaluate : 4.793 ------------------------------------------------------------------------------- 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 B residue 76 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 196 PHE 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 I residue 256 LEU 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 M residue 21 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 261 LYS Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 209 GLU 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 207 THR Chi-restraints excluded: chain R residue 236 CYS 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 S residue 74 VAL Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 287 ASP 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 424 LEU Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 405 ASP Chi-restraints excluded: chain U residue 241 ASN 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 404 ARG Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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 s residue 578 LEU Chi-restraints excluded: chain t residue 575 TYR Chi-restraints excluded: chain u residue 580 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 455 optimal weight: 40.0000 chunk 352 optimal weight: 0.6980 chunk 524 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 620 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 442 GLN C 33 ASN C 93 GLN C 135 ASN D 269 GLN F 269 GLN G 206 ASN J 22 GLN J 38 GLN K 77 HIS K 206 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 295 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 62692 Z= 0.357 Angle : 0.645 11.890 86986 Z= 0.346 Chirality : 0.044 0.343 9900 Planarity : 0.005 0.059 9171 Dihedral : 21.918 179.882 14224 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.99 % Allowed : 15.41 % Favored : 81.60 % 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: 0.68 (0.11), residues: 6033 helix: 0.87 (0.09), residues: 3310 sheet: -0.26 (0.22), residues: 477 loop : 0.19 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 225 HIS 0.009 0.001 HIS L 77 PHE 0.029 0.002 PHE S 306 TYR 0.032 0.002 TYR R 233 ARG 0.010 0.001 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 808 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 649 time to evaluate : 4.901 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: 0.8598 (OUTLIER) cc_final: 0.8395 (ttmm) REVERT: A 275 ARG cc_start: 0.7779 (tmm160) cc_final: 0.6880 (tpp80) REVERT: A 362 LYS cc_start: 0.7892 (mptt) cc_final: 0.7665 (mmtt) REVERT: A 416 GLN cc_start: 0.7848 (tp40) cc_final: 0.7531 (tp-100) REVERT: A 456 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: A 492 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7378 (ttp80) REVERT: A 539 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8441 (mppt) REVERT: B 20 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: B 49 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.7747 (tmtt) REVERT: B 89 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7569 (mpp-170) REVERT: C 156 MET cc_start: 0.9050 (ttm) cc_final: 0.8797 (ttm) REVERT: D 74 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6478 (ttm170) REVERT: D 107 LYS cc_start: 0.8158 (ttpp) cc_final: 0.7479 (ttpp) REVERT: E 38 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: E 76 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6505 (ttp-170) REVERT: E 131 GLU cc_start: 0.8117 (tp30) cc_final: 0.7887 (mm-30) REVERT: E 225 LYS cc_start: 0.6974 (tptp) cc_final: 0.6626 (tmmt) REVERT: E 231 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7874 (ttp80) REVERT: E 270 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6961 (mp0) REVERT: F 74 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7589 (ppt-90) REVERT: F 80 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.5043 (mp-120) REVERT: F 209 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: F 213 GLN cc_start: 0.7479 (mt0) cc_final: 0.7143 (mt0) REVERT: F 273 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7873 (mtpt) REVERT: G 269 GLN cc_start: 0.7576 (mm110) cc_final: 0.7113 (mt0) REVERT: H 261 LYS cc_start: 0.8071 (mptt) cc_final: 0.7483 (mptm) REVERT: I 114 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7780 (mtpp) REVERT: J 78 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7367 (mmmt) REVERT: J 196 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8203 (t80) REVERT: K 175 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8065 (ttt90) REVERT: K 196 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8859 (t80) REVERT: L 76 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7534 (mtp180) REVERT: L 225 LYS cc_start: 0.8084 (pptt) cc_final: 0.7725 (ptmm) REVERT: L 246 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6954 (mp0) REVERT: M 21 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7133 (tp) REVERT: M 184 GLU cc_start: 0.8004 (tt0) cc_final: 0.7324 (pt0) REVERT: M 205 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7451 (mttt) REVERT: M 211 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.7115 (t-100) REVERT: M 214 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6842 (ptp) REVERT: M 223 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5508 (m110) REVERT: O 269 GLN cc_start: 0.7497 (tp40) cc_final: 0.7145 (tp-100) REVERT: O 273 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7408 (mtmt) REVERT: P 181 LYS cc_start: 0.7801 (ptmm) cc_final: 0.6864 (pttt) REVERT: Q 63 ARG cc_start: 0.6257 (mmt90) cc_final: 0.5541 (mmp-170) REVERT: Q 128 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6418 (tpt170) REVERT: Q 229 MET cc_start: 0.3033 (mpt) cc_final: 0.1840 (tpp) REVERT: Q 262 LYS cc_start: 0.4648 (OUTLIER) cc_final: 0.4236 (ptmm) REVERT: R 104 LYS cc_start: 0.7686 (mttt) cc_final: 0.6771 (ttmm) REVERT: R 165 GLU cc_start: 0.8657 (tp30) cc_final: 0.8355 (tp30) REVERT: R 188 ARG cc_start: 0.7502 (ttm170) cc_final: 0.6718 (tmm160) REVERT: R 316 GLU cc_start: 0.7907 (mp0) cc_final: 0.7608 (mp0) REVERT: R 381 MET cc_start: 0.8627 (mmm) cc_final: 0.8379 (mmm) REVERT: R 431 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: R 480 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: S 76 LEU cc_start: 0.7257 (pt) cc_final: 0.6761 (tt) REVERT: S 268 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: S 295 ASN cc_start: 0.7916 (m-40) cc_final: 0.7552 (m-40) REVERT: S 299 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5963 (mt0) REVERT: S 349 ASP cc_start: 0.6831 (t70) cc_final: 0.6559 (t0) REVERT: S 384 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: T 219 GLU cc_start: 0.5452 (mp0) cc_final: 0.3374 (mp0) REVERT: T 268 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: T 338 TYR cc_start: 0.6909 (p90) cc_final: 0.6392 (p90) REVERT: T 373 TYR cc_start: 0.5468 (OUTLIER) cc_final: 0.4571 (t80) REVERT: T 411 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7007 (mtp) REVERT: T 434 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: U 201 VAL cc_start: 0.5386 (OUTLIER) cc_final: 0.5091 (t) REVERT: U 241 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: U 300 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8379 (mp) REVERT: U 372 ARG cc_start: 0.6284 (ttp80) cc_final: 0.5537 (ttp-110) REVERT: U 404 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5448 (mmp-170) REVERT: U 434 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: U 473 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.5993 (m90) REVERT: r 575 TYR cc_start: 0.2939 (OUTLIER) cc_final: 0.2213 (m-80) REVERT: s 578 LEU cc_start: 0.2451 (OUTLIER) cc_final: 0.2016 (tp) REVERT: t 575 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.3481 (m-80) outliers start: 159 outliers final: 73 residues processed: 758 average time/residue: 1.6816 time to fit residues: 1573.8253 Evaluate side-chains 734 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 622 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP 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 B residue 76 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 74 ARG 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 E residue 38 GLN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 273 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER 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 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 256 LEU 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 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 21 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP 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 180 ILE Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 64 THR 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 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 183 ASP 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 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 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 431 TYR Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 268 GLU 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 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 424 LEU Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 268 GLU Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 358 LEU 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 434 GLU Chi-restraints excluded: chain U residue 196 ASP Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 241 ASN 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 327 LEU Chi-restraints excluded: chain U residue 364 LEU Chi-restraints excluded: chain U residue 404 ARG 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 485 ASP 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 s residue 578 LEU 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: 5.9990 chunk 247 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 394 optimal weight: 2.9990 chunk 422 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 487 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 442 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN D 269 GLN F 269 GLN G 206 ASN J 38 GLN K 206 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN Q 185 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 62692 Z= 0.267 Angle : 0.601 12.547 86986 Z= 0.322 Chirality : 0.042 0.312 9900 Planarity : 0.005 0.058 9171 Dihedral : 21.875 179.410 14224 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.57 % Allowed : 16.23 % Favored : 81.19 % 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: 0.73 (0.11), residues: 6033 helix: 0.92 (0.09), residues: 3302 sheet: -0.23 (0.22), residues: 484 loop : 0.19 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP T 225 HIS 0.007 0.001 HIS L 77 PHE 0.021 0.002 PHE S 306 TYR 0.025 0.002 TYR R 233 ARG 0.012 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 775 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 638 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7454 (tmt-80) REVERT: A 275 ARG cc_start: 0.7749 (tmm160) cc_final: 0.6855 (tpp80) REVERT: A 362 LYS cc_start: 0.7880 (mptt) cc_final: 0.7665 (mmtt) REVERT: A 416 GLN cc_start: 0.7811 (tp40) cc_final: 0.7507 (tp-100) REVERT: A 456 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: A 492 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7344 (ttp80) REVERT: A 539 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8437 (mppt) REVERT: B 20 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: B 49 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7766 (tmtt) REVERT: B 89 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7551 (mpp-170) REVERT: C 156 MET cc_start: 0.9002 (ttm) cc_final: 0.8660 (ttt) REVERT: D 74 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6423 (ttm170) REVERT: D 107 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7469 (ttpp) REVERT: E 38 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: E 76 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6478 (ttp-170) REVERT: E 131 GLU cc_start: 0.8086 (tp30) cc_final: 0.7856 (mm-30) REVERT: E 225 LYS cc_start: 0.6938 (tptp) cc_final: 0.6582 (tmmt) REVERT: E 231 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7872 (ttp80) REVERT: E 270 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6951 (mp0) REVERT: F 74 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7562 (ppt-90) REVERT: F 209 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: F 213 GLN cc_start: 0.7466 (mt0) cc_final: 0.7111 (mt0) REVERT: F 273 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7860 (mtpt) REVERT: G 269 GLN cc_start: 0.7602 (mm110) cc_final: 0.7137 (mt0) REVERT: H 261 LYS cc_start: 0.8078 (mptt) cc_final: 0.7488 (mptm) REVERT: I 114 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: J 78 LYS cc_start: 0.7698 (mmmm) cc_final: 0.7408 (mmmt) REVERT: J 196 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8206 (t80) REVERT: J 206 ASN cc_start: 0.8067 (m-40) cc_final: 0.7667 (m110) REVERT: K 99 LYS cc_start: 0.8909 (mttp) cc_final: 0.8212 (mmpt) REVERT: K 175 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8115 (ttp80) REVERT: K 196 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8829 (t80) REVERT: K 214 MET cc_start: 0.8432 (mtp) cc_final: 0.8057 (mtt) REVERT: K 225 LYS cc_start: 0.7502 (ttpm) cc_final: 0.7266 (ttmt) REVERT: L 225 LYS cc_start: 0.8099 (pptt) cc_final: 0.7760 (ptmm) REVERT: L 246 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6871 (mp0) REVERT: M 21 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7108 (tp) REVERT: M 175 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.7159 (tpt90) REVERT: M 184 GLU cc_start: 0.8013 (tt0) cc_final: 0.7369 (pt0) REVERT: M 205 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7455 (mttt) REVERT: M 211 TRP cc_start: 0.7626 (OUTLIER) cc_final: 0.7063 (t-100) REVERT: M 214 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: M 223 ASN cc_start: 0.5786 (OUTLIER) cc_final: 0.5463 (m110) REVERT: M 273 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7791 (tptt) REVERT: N 119 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7785 (mtmt) REVERT: O 37 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7403 (tm130) REVERT: O 210 MET cc_start: 0.6799 (mtp) cc_final: 0.6414 (mtt) REVERT: O 269 GLN cc_start: 0.7522 (tp40) cc_final: 0.7277 (tp-100) REVERT: P 181 LYS cc_start: 0.7787 (ptmm) cc_final: 0.6859 (pttt) REVERT: Q 63 ARG cc_start: 0.6264 (mmt90) cc_final: 0.5541 (mmp-170) REVERT: Q 128 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6421 (tpt170) REVERT: Q 229 MET cc_start: 0.3032 (mpt) cc_final: 0.1835 (tpp) REVERT: R 165 GLU cc_start: 0.8646 (tp30) cc_final: 0.8405 (tp30) REVERT: R 188 ARG cc_start: 0.7468 (ttm170) cc_final: 0.6687 (tmm160) REVERT: R 312 ASP cc_start: 0.6746 (t0) cc_final: 0.6386 (t0) REVERT: R 316 GLU cc_start: 0.7853 (mp0) cc_final: 0.7582 (mp0) REVERT: R 381 MET cc_start: 0.8631 (mmm) cc_final: 0.8329 (mmm) REVERT: R 480 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: S 76 LEU cc_start: 0.7244 (pt) cc_final: 0.6765 (tt) REVERT: S 268 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8116 (pp20) REVERT: S 349 ASP cc_start: 0.6824 (t70) cc_final: 0.6555 (t0) REVERT: S 384 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: S 430 MET cc_start: 0.7816 (mmt) cc_final: 0.7569 (mmm) REVERT: S 458 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7478 (m) REVERT: T 268 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: T 338 TYR cc_start: 0.6940 (p90) cc_final: 0.6423 (p90) REVERT: T 373 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4588 (t80) REVERT: T 411 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6965 (mtp) REVERT: U 241 ASN cc_start: 0.5691 (OUTLIER) cc_final: 0.5486 (m-40) REVERT: U 300 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8375 (mp) REVERT: U 372 ARG cc_start: 0.6284 (ttp80) cc_final: 0.5526 (ttp-110) REVERT: U 434 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: U 473 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5993 (m90) REVERT: r 575 TYR cc_start: 0.2921 (OUTLIER) cc_final: 0.2204 (m-80) REVERT: s 578 LEU cc_start: 0.2449 (OUTLIER) cc_final: 0.1993 (tp) REVERT: t 575 TYR cc_start: 0.5125 (OUTLIER) cc_final: 0.3478 (m-80) outliers start: 137 outliers final: 75 residues processed: 728 average time/residue: 1.7203 time to fit residues: 1544.9511 Evaluate side-chains 728 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 620 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 206 ASP 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 A residue 464 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 74 ARG 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 E residue 38 GLN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 273 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 196 PHE 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 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 273 LYS 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 M residue 21 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP 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 33 ILE Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 34 VAL 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 183 ASP Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain R residue 46 LEU 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 245 ASP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 238 MET Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 351 GLU 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 424 LEU Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 268 GLU 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 511 VAL Chi-restraints excluded: chain U residue 196 ASP Chi-restraints excluded: chain U residue 241 ASN 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 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 485 ASP 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 s residue 578 LEU 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: 8.9990 chunk 594 optimal weight: 5.9990 chunk 542 optimal weight: 0.9990 chunk 578 optimal weight: 0.0870 chunk 348 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 454 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 522 optimal weight: 9.9990 chunk 547 optimal weight: 9.9990 chunk 576 optimal weight: 50.0000 overall best weight: 2.1764 ------------------------------------------------------------------------------- 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 C 33 ASN C 93 GLN D 269 GLN F 269 GLN G 206 ASN H 185 GLN J 38 GLN J 213 GLN K 206 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN R 295 ASN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN S 295 ASN ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 62692 Z= 0.173 Angle : 0.554 13.193 86986 Z= 0.296 Chirality : 0.039 0.324 9900 Planarity : 0.004 0.061 9171 Dihedral : 21.755 179.779 14224 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.29 % Allowed : 16.91 % Favored : 80.80 % 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: 1.04 (0.11), residues: 6033 helix: 1.20 (0.09), residues: 3301 sheet: -0.10 (0.22), residues: 502 loop : 0.29 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP T 225 HIS 0.007 0.001 HIS R 283 PHE 0.014 0.001 PHE S 306 TYR 0.015 0.001 TYR T 459 ARG 0.013 0.000 ARG U 493 *********************** 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 775 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 653 time to evaluate : 4.888 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 246 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (ttmm) REVERT: A 275 ARG cc_start: 0.7709 (tmm160) cc_final: 0.6805 (tpp80) REVERT: A 362 LYS cc_start: 0.7831 (mptt) cc_final: 0.7604 (mmtt) REVERT: A 416 GLN cc_start: 0.7773 (tp40) cc_final: 0.7489 (tp-100) REVERT: A 456 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: A 492 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7306 (ttp80) REVERT: A 539 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8421 (mppt) REVERT: B 20 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 49 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.7787 (tmtt) REVERT: C 156 MET cc_start: 0.8928 (ttm) cc_final: 0.8659 (ttt) REVERT: D 74 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6400 (ttm170) REVERT: D 107 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7444 (ttpp) REVERT: E 38 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: E 76 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6445 (ttp-170) REVERT: E 131 GLU cc_start: 0.8097 (tp30) cc_final: 0.7880 (mm-30) REVERT: E 225 LYS cc_start: 0.6863 (tptp) cc_final: 0.6554 (tmmt) REVERT: E 231 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7775 (ttp80) REVERT: E 270 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6878 (mp0) REVERT: F 74 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7430 (ppt-90) REVERT: F 209 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: F 213 GLN cc_start: 0.7382 (mt0) cc_final: 0.7059 (mt0) REVERT: F 273 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: G 269 GLN cc_start: 0.7582 (mm110) cc_final: 0.7119 (mt0) REVERT: H 261 LYS cc_start: 0.8088 (mptt) cc_final: 0.7484 (mptm) REVERT: I 78 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6837 (pmtt) REVERT: I 114 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7682 (mtpp) REVERT: J 78 LYS cc_start: 0.7645 (mmmm) cc_final: 0.7421 (mmmt) REVERT: J 196 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8197 (t80) REVERT: J 206 ASN cc_start: 0.8065 (m-40) cc_final: 0.7675 (m110) REVERT: K 61 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7581 (mp0) REVERT: K 99 LYS cc_start: 0.8917 (mttp) cc_final: 0.8218 (mmpt) REVERT: K 175 ARG cc_start: 0.8342 (ttm170) cc_final: 0.8058 (ttp80) REVERT: K 196 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8636 (t80) REVERT: L 225 LYS cc_start: 0.8057 (pptt) cc_final: 0.7775 (ptmm) REVERT: L 246 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6783 (mp0) REVERT: M 21 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7103 (tp) REVERT: M 175 ARG cc_start: 0.7410 (tpt-90) cc_final: 0.7083 (tpt170) REVERT: M 184 GLU cc_start: 0.7933 (tt0) cc_final: 0.7311 (pt0) REVERT: M 205 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7438 (mttt) REVERT: M 209 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6173 (tt0) REVERT: M 211 TRP cc_start: 0.7594 (t-100) cc_final: 0.6957 (t-100) REVERT: M 214 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7000 (mpp) REVERT: M 223 ASN cc_start: 0.5737 (OUTLIER) cc_final: 0.5421 (m110) REVERT: M 273 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7785 (tptt) REVERT: O 210 MET cc_start: 0.6996 (mtp) cc_final: 0.6689 (mtt) REVERT: O 229 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4968 (mtp) REVERT: P 181 LYS cc_start: 0.7683 (ptmm) cc_final: 0.6776 (pttt) REVERT: P 205 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6720 (mmmt) REVERT: Q 128 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6393 (tpt170) REVERT: Q 229 MET cc_start: 0.3029 (mpt) cc_final: 0.1846 (tpp) REVERT: Q 262 LYS cc_start: 0.4619 (OUTLIER) cc_final: 0.4274 (ptmm) REVERT: R 165 GLU cc_start: 0.8669 (tp30) cc_final: 0.8392 (tp30) REVERT: R 188 ARG cc_start: 0.7495 (ttm170) cc_final: 0.6719 (tmm160) REVERT: R 191 LYS cc_start: 0.7882 (tmtt) cc_final: 0.7650 (tptp) REVERT: R 312 ASP cc_start: 0.6715 (t0) cc_final: 0.6327 (t0) REVERT: R 316 GLU cc_start: 0.7794 (mp0) cc_final: 0.7525 (mp0) REVERT: R 381 MET cc_start: 0.8653 (mmm) cc_final: 0.8358 (mmm) REVERT: S 76 LEU cc_start: 0.7212 (pt) cc_final: 0.6736 (tt) REVERT: S 268 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: S 299 GLN cc_start: 0.6689 (tp-100) cc_final: 0.5850 (mp-120) REVERT: S 349 ASP cc_start: 0.6805 (t70) cc_final: 0.6529 (t0) REVERT: T 215 ASP cc_start: 0.7103 (t0) cc_final: 0.6746 (t0) REVERT: T 338 TYR cc_start: 0.6886 (p90) cc_final: 0.6449 (p90) REVERT: T 373 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.4617 (t80) REVERT: T 492 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7681 (ttp80) REVERT: U 201 VAL cc_start: 0.5291 (OUTLIER) cc_final: 0.4997 (t) REVERT: U 238 MET cc_start: 0.2926 (ptm) cc_final: 0.2292 (pmm) REVERT: U 300 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8339 (mp) REVERT: U 372 ARG cc_start: 0.6252 (ttp80) cc_final: 0.5489 (ttp-110) REVERT: U 434 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: U 473 HIS cc_start: 0.6479 (OUTLIER) cc_final: 0.5872 (m90) REVERT: r 575 TYR cc_start: 0.2879 (OUTLIER) cc_final: 0.2200 (m-80) REVERT: s 578 LEU cc_start: 0.2398 (OUTLIER) cc_final: 0.1952 (tp) REVERT: t 575 TYR cc_start: 0.5103 (OUTLIER) cc_final: 0.3590 (m-80) outliers start: 122 outliers final: 53 residues processed: 735 average time/residue: 1.7068 time to fit residues: 1551.0334 Evaluate side-chains 715 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 632 time to evaluate : 4.818 ------------------------------------------------------------------------------- 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 B residue 76 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 273 LYS Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 40 LYS 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 I residue 256 LEU 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 273 LYS Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 180 ILE 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 180 ILE Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 249 ARG Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 180 ILE 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 183 ASP 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 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 268 GLU 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 455 THR Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR 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 U residue 201 VAL 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 424 LEU Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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 578 LEU 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: 0.7980 chunk 611 optimal weight: 4.9990 chunk 373 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 425 optimal weight: 0.0770 chunk 641 optimal weight: 7.9990 chunk 590 optimal weight: 0.9990 chunk 510 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 313 optimal weight: 0.0470 overall best weight: 1.1840 ------------------------------------------------------------------------------- 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 415 GLN A 431 ASN A 442 GLN C 33 ASN C 93 GLN D 269 GLN F 269 GLN G 206 ASN J 38 GLN J 213 GLN K 206 ASN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 374 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 62692 Z= 0.150 Angle : 0.540 12.823 86986 Z= 0.288 Chirality : 0.038 0.295 9900 Planarity : 0.004 0.060 9171 Dihedral : 21.653 179.850 14224 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 17.81 % Favored : 80.57 % 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: 1.27 (0.11), residues: 6033 helix: 1.38 (0.09), residues: 3325 sheet: -0.06 (0.22), residues: 521 loop : 0.42 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 225 HIS 0.006 0.001 HIS R 283 PHE 0.011 0.001 PHE U 284 TYR 0.014 0.001 TYR R 435 ARG 0.013 0.000 ARG U 493 ********************** 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 752 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 666 time to evaluate : 4.938 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: 0.8463 (OUTLIER) cc_final: 0.8152 (ttmm) REVERT: A 275 ARG cc_start: 0.7707 (tmm160) cc_final: 0.6809 (tpp80) REVERT: A 362 LYS cc_start: 0.7809 (mptt) cc_final: 0.7575 (mmtt) REVERT: A 397 GLU cc_start: 0.8209 (tt0) cc_final: 0.7996 (tt0) REVERT: A 416 GLN cc_start: 0.7769 (tp40) cc_final: 0.7498 (tp-100) REVERT: A 456 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: A 492 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7289 (ttp80) REVERT: A 539 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8437 (mppt) REVERT: A 551 MET cc_start: 0.8124 (mmm) cc_final: 0.7876 (mmm) REVERT: B 20 GLU cc_start: 0.7700 (pm20) cc_final: 0.7380 (mp0) REVERT: B 49 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.7784 (tmtt) REVERT: C 156 MET cc_start: 0.8823 (ttm) cc_final: 0.8542 (ttt) REVERT: D 74 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6246 (ttm170) REVERT: D 107 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7398 (ttpp) REVERT: E 131 GLU cc_start: 0.8089 (tp30) cc_final: 0.7887 (mm-30) REVERT: E 225 LYS cc_start: 0.6489 (tptp) cc_final: 0.6282 (tmmt) REVERT: E 231 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7745 (ttp80) REVERT: E 270 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6815 (mp0) REVERT: F 74 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7432 (ppt-90) REVERT: F 227 LYS cc_start: 0.7503 (ttmm) cc_final: 0.7248 (ttpp) REVERT: G 269 GLN cc_start: 0.7563 (mm110) cc_final: 0.7092 (mt0) REVERT: H 202 GLU cc_start: 0.7650 (tp30) cc_final: 0.7311 (tp30) REVERT: H 261 LYS cc_start: 0.8054 (mptt) cc_final: 0.7497 (mptm) REVERT: I 78 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6956 (pmtt) REVERT: J 78 LYS cc_start: 0.7603 (mmmm) cc_final: 0.7393 (mmmt) REVERT: J 196 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8190 (t80) REVERT: J 206 ASN cc_start: 0.8034 (m-40) cc_final: 0.7636 (m110) REVERT: K 61 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7576 (mp0) REVERT: K 99 LYS cc_start: 0.8902 (mttp) cc_final: 0.8204 (mmpt) REVERT: K 116 ARG cc_start: 0.8841 (mmp80) cc_final: 0.8535 (mmt90) REVERT: K 175 ARG cc_start: 0.8319 (ttm170) cc_final: 0.8044 (ttp80) REVERT: K 196 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8628 (t80) REVERT: L 127 ASP cc_start: 0.8635 (m-30) cc_final: 0.8431 (m-30) REVERT: L 225 LYS cc_start: 0.8016 (pptt) cc_final: 0.7789 (ptmm) REVERT: L 246 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6763 (mp0) REVERT: L 273 LYS cc_start: 0.7447 (pptt) cc_final: 0.7025 (tmmt) REVERT: M 21 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7139 (tp) REVERT: M 175 ARG cc_start: 0.7374 (tpt-90) cc_final: 0.7065 (tpt170) REVERT: M 184 GLU cc_start: 0.7878 (tt0) cc_final: 0.7516 (pm20) REVERT: M 205 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7544 (mttt) REVERT: M 211 TRP cc_start: 0.7602 (t-100) cc_final: 0.6895 (t-100) REVERT: M 214 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6952 (ptp) REVERT: M 268 LEU cc_start: 0.6864 (tp) cc_final: 0.6138 (mp) REVERT: M 269 GLN cc_start: 0.6540 (mt0) cc_final: 0.5861 (mm-40) REVERT: M 273 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7746 (tptt) REVERT: N 119 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7665 (mtmt) REVERT: O 210 MET cc_start: 0.6981 (mtp) cc_final: 0.6740 (mtt) REVERT: O 214 MET cc_start: 0.6458 (pmt) cc_final: 0.6115 (pmm) REVERT: O 229 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.4902 (mtp) REVERT: P 181 LYS cc_start: 0.7690 (ptmm) cc_final: 0.6754 (pttt) REVERT: P 205 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6786 (mmmt) REVERT: Q 229 MET cc_start: 0.3021 (mpt) cc_final: 0.1859 (tpp) REVERT: Q 262 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.4269 (ptmm) REVERT: R 165 GLU cc_start: 0.8632 (tp30) cc_final: 0.8296 (tp30) REVERT: R 166 LYS cc_start: 0.8379 (mmpt) cc_final: 0.8149 (mmpt) REVERT: R 188 ARG cc_start: 0.7519 (ttm170) cc_final: 0.6726 (tmm160) REVERT: R 191 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7664 (tptp) REVERT: R 312 ASP cc_start: 0.6621 (t0) cc_final: 0.6241 (t0) REVERT: R 316 GLU cc_start: 0.7774 (mp0) cc_final: 0.7559 (mp0) REVERT: R 381 MET cc_start: 0.8705 (mmm) cc_final: 0.8374 (mmm) REVERT: S 76 LEU cc_start: 0.7244 (pt) cc_final: 0.6755 (tt) REVERT: S 268 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: S 349 ASP cc_start: 0.6810 (t70) cc_final: 0.6552 (t0) REVERT: T 215 ASP cc_start: 0.7014 (t0) cc_final: 0.6755 (t0) REVERT: T 355 ARG cc_start: 0.7599 (tmm160) cc_final: 0.7310 (tpt90) REVERT: T 373 TYR cc_start: 0.5323 (m-80) cc_final: 0.4663 (t80) REVERT: U 201 VAL cc_start: 0.5266 (OUTLIER) cc_final: 0.4988 (t) REVERT: U 238 MET cc_start: 0.2970 (ptm) cc_final: 0.2463 (pmm) REVERT: U 300 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8342 (mp) REVERT: U 372 ARG cc_start: 0.6225 (ttp80) cc_final: 0.5473 (ttp-110) REVERT: U 434 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: U 473 HIS cc_start: 0.6433 (OUTLIER) cc_final: 0.5828 (m90) REVERT: r 575 TYR cc_start: 0.2804 (OUTLIER) cc_final: 0.2320 (m-80) REVERT: s 578 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.1958 (tp) REVERT: t 575 TYR cc_start: 0.5045 (OUTLIER) cc_final: 0.3566 (m-80) outliers start: 86 outliers final: 47 residues processed: 726 average time/residue: 1.7353 time to fit residues: 1554.7376 Evaluate side-chains 701 residues out of total 5322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 634 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 110 THR 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 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 256 LEU 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 237 THR Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain M residue 261 LYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 180 ILE Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 183 ASP 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 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 245 ASP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain U residue 201 VAL 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 473 HIS Chi-restraints excluded: chain U residue 485 ASP 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 578 LEU 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: 6.9990 chunk 544 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 471 optimal weight: 40.0000 chunk 75 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 511 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 525 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 442 GLN C 33 ASN C 93 GLN D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 213 GLN K 206 ASN ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN ** Q 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 465 GLN ** U 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 374 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154479 restraints weight = 76522.061| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.63 r_work: 0.3722 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 62692 Z= 0.199 Angle : 0.563 12.733 86986 Z= 0.300 Chirality : 0.040 0.293 9900 Planarity : 0.004 0.061 9171 Dihedral : 21.706 179.827 14222 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.77 % Allowed : 17.91 % Favored : 80.33 % 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: 1.19 (0.11), residues: 6033 helix: 1.31 (0.09), residues: 3319 sheet: -0.03 (0.22), residues: 507 loop : 0.39 (0.14), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 225 HIS 0.005 0.001 HIS L 77 PHE 0.019 0.001 PHE S 306 TYR 0.021 0.001 TYR R 233 ARG 0.013 0.000 ARG S 143 =============================================================================== Job complete usr+sys time: 24363.18 seconds wall clock time: 420 minutes 28.27 seconds (25228.27 seconds total)