Starting phenix.real_space_refine on Mon Jul 6 00:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibf_35342/07_2026/8ibf_35342.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 244 5.16 5 C 20903 2.51 5 N 5129 2.21 5 O 5649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31948 Number of models: 1 Model: "" Number of chains: 36 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 350 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain: "J" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1229 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain breaks: 2 Chain: "K" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 729 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 4798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4798 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Chain: "M" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3630 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain: "N" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2694 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain: "O" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2599 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "U" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 718 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "X" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 4, 'TRANS': 22} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1030 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "c" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 439 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 858 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 802 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 6, 'TRANS': 58} Chain: "k" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "l" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 18, 'TRANS': 137} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1541 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "o" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1050 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "p" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1452 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 245 Unusual residues: {'3PE': 4, 'CDL': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "M" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "d" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "h" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "m" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "n" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 6.77, per 1000 atoms: 0.21 Number of scatterers: 31948 At special positions: 0 Unit cell: (185.9, 139.7, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 244 16.00 P 23 15.00 O 5649 8.00 N 5129 7.00 C 20903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS Y 20 " - pdb=" SG CYS Y 77 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 97 " - pdb=" SG CYS Y 117 " distance=2.36 Simple disulfide: pdb=" SG CYS e 33 " - pdb=" SG CYS e 66 " distance=2.03 Simple disulfide: pdb=" SG CYS e 43 " - pdb=" SG CYS e 56 " distance=2.05 Simple disulfide: pdb=" SG CYS o 59 " - pdb=" SG CYS o 90 " distance=2.03 Simple disulfide: pdb=" SG CYS o 69 " - pdb=" SG CYS o 80 " distance=2.36 Simple disulfide: pdb=" SG CYS p 77 " - pdb=" SG CYS p 84 " distance=2.05 Simple disulfide: pdb=" SG CYS p 113 " - pdb=" SG CYS p 125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7274 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 4 sheets defined 67.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.747A pdb=" N GLN D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'J' and resid 4 through 21 removed outlier: 3.824A pdb=" N LEU J 8 " --> pdb=" O TYR J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 46 removed outlier: 3.578A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 Processing helix chain 'J' and resid 62 through 74 Processing helix chain 'J' and resid 84 through 110 removed outlier: 3.987A pdb=" N VAL J 100 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 removed outlier: 3.505A pdb=" N TYR J 145 " --> pdb=" O ALA J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 171 removed outlier: 4.067A pdb=" N MET J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 153 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.548A pdb=" N ASN K 7 " --> pdb=" O SER K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 51 removed outlier: 4.202A pdb=" N THR K 29 " --> pdb=" O HIS K 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 85 removed outlier: 3.810A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU K 64 " --> pdb=" O PRO K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'L' and resid 2 through 24 removed outlier: 4.114A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 25 through 30 removed outlier: 4.418A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 58 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 83 through 108 removed outlier: 3.575A pdb=" N GLN L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 133 Processing helix chain 'L' and resid 136 through 156 removed outlier: 3.548A pdb=" N LEU L 140 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 191 removed outlier: 3.608A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 202 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 237 removed outlier: 3.677A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 247 Processing helix chain 'L' and resid 250 through 263 removed outlier: 3.535A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 270 removed outlier: 4.060A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 295 removed outlier: 3.837A pdb=" N LEU L 274 " --> pdb=" O ASN L 270 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN L 295 " --> pdb=" O CYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 319 Processing helix chain 'L' and resid 321 through 350 removed outlier: 3.503A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 Processing helix chain 'L' and resid 361 through 366 Processing helix chain 'L' and resid 366 through 381 Processing helix chain 'L' and resid 386 through 402 removed outlier: 3.531A pdb=" N TYR L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 431 Processing helix chain 'L' and resid 447 through 472 Proline residue: L 453 - end of helix removed outlier: 5.301A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 488 Processing helix chain 'L' and resid 488 through 509 removed outlier: 3.899A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 525 removed outlier: 3.707A pdb=" N SER L 521 " --> pdb=" O ASN L 517 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE L 522 " --> pdb=" O PRO L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 534 removed outlier: 3.562A pdb=" N HIS L 534 " --> pdb=" O PRO L 530 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 548 removed outlier: 3.628A pdb=" N LEU L 542 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 544 " --> pdb=" O LYS L 540 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER L 545 " --> pdb=" O SER L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 561 Processing helix chain 'L' and resid 562 through 579 removed outlier: 3.683A pdb=" N THR L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER L 567 " --> pdb=" O PRO L 563 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 605 removed outlier: 3.502A pdb=" N TYR L 587 " --> pdb=" O LEU L 583 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 Processing helix chain 'M' and resid 10 through 18 Processing helix chain 'M' and resid 22 through 39 Processing helix chain 'M' and resid 40 through 43 Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.506A pdb=" N ILE M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU M 68 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 91 through 111 removed outlier: 3.577A pdb=" N GLN M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 125 Processing helix chain 'M' and resid 125 through 137 removed outlier: 3.542A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 172 removed outlier: 3.851A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 191 through 207 removed outlier: 3.936A pdb=" N LEU M 197 " --> pdb=" O ASN M 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 223 removed outlier: 3.744A pdb=" N GLU M 222 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 234 Processing helix chain 'M' and resid 234 through 247 removed outlier: 4.145A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 258 removed outlier: 3.511A pdb=" N ALA M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.505A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 Processing helix chain 'M' and resid 305 through 338 Processing helix chain 'M' and resid 347 through 351 Processing helix chain 'M' and resid 352 through 367 removed outlier: 3.518A pdb=" N ALA M 356 " --> pdb=" O PHE M 352 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR M 357 " --> pdb=" O PRO M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 389 Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.145A pdb=" N LEU M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE M 400 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE M 401 " --> pdb=" O GLY M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 450 Proline residue: M 443 - end of helix removed outlier: 3.763A pdb=" N SER M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 455 Processing helix chain 'N' and resid 2 through 23 Proline residue: N 17 - end of helix removed outlier: 3.553A pdb=" N THR N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 removed outlier: 3.530A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.579A pdb=" N GLU N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS N 79 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 106 Processing helix chain 'N' and resid 108 through 112 removed outlier: 3.531A pdb=" N PHE N 111 " --> pdb=" O LEU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 3.866A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 135 through 146 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'N' and resid 150 through 172 removed outlier: 3.878A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 194 removed outlier: 3.534A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 222 removed outlier: 3.802A pdb=" N THR N 201 " --> pdb=" O ASN N 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU N 203 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.751A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 232 Processing helix chain 'N' and resid 232 through 237 Processing helix chain 'N' and resid 239 through 252 removed outlier: 4.195A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 273 removed outlier: 4.129A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 301 removed outlier: 3.835A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 317 Processing helix chain 'N' and resid 323 through 335 removed outlier: 4.323A pdb=" N SER N 327 " --> pdb=" O ASN N 323 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET N 332 " --> pdb=" O THR N 328 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 333 " --> pdb=" O LEU N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 338 No H-bonds generated for 'chain 'N' and resid 336 through 338' Processing helix chain 'N' and resid 339 through 344 removed outlier: 3.631A pdb=" N LEU N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 45 Processing helix chain 'O' and resid 49 through 53 Processing helix chain 'O' and resid 69 through 82 removed outlier: 3.674A pdb=" N LEU O 73 " --> pdb=" O GLY O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 98 Processing helix chain 'O' and resid 113 through 120 Processing helix chain 'O' and resid 126 through 153 Processing helix chain 'O' and resid 162 through 176 removed outlier: 4.104A pdb=" N PHE O 167 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL O 168 " --> pdb=" O TYR O 164 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE O 169 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU O 170 " --> pdb=" O ASP O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 195 Processing helix chain 'O' and resid 196 through 198 No H-bonds generated for 'chain 'O' and resid 196 through 198' Processing helix chain 'O' and resid 210 through 221 Processing helix chain 'O' and resid 230 through 244 Processing helix chain 'O' and resid 244 through 253 removed outlier: 4.122A pdb=" N GLU O 251 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET O 252 " --> pdb=" O LYS O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 276 Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 287 through 299 removed outlier: 4.567A pdb=" N TYR O 293 " --> pdb=" O TRP O 289 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 294 " --> pdb=" O THR O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 300 through 305 Processing helix chain 'O' and resid 306 through 310 removed outlier: 3.651A pdb=" N ILE O 310 " --> pdb=" O TYR O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 332 Processing helix chain 'U' and resid 75 through 88 removed outlier: 3.551A pdb=" N ASP U 81 " --> pdb=" O ASP U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 126 removed outlier: 3.739A pdb=" N GLU U 117 " --> pdb=" O LEU U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 136 Processing helix chain 'U' and resid 142 through 152 removed outlier: 3.519A pdb=" N ALA U 149 " --> pdb=" O VAL U 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.901A pdb=" N TYR Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N HIS Y 12 " --> pdb=" O PHE Y 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 45 Processing helix chain 'Y' and resid 50 through 84 Processing helix chain 'Y' and resid 88 through 107 removed outlier: 3.766A pdb=" N TYR Y 92 " --> pdb=" O ASP Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 134 Processing helix chain 'c' and resid 40 through 73 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 28 through 49 Processing helix chain 'd' and resid 57 through 97 removed outlier: 3.609A pdb=" N LEU d 62 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG d 78 " --> pdb=" O PHE d 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 11 Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 33 through 42 removed outlier: 3.605A pdb=" N LYS e 38 " --> pdb=" O HIS e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 52 Processing helix chain 'e' and resid 54 through 56 No H-bonds generated for 'chain 'e' and resid 54 through 56' Processing helix chain 'e' and resid 57 through 67 removed outlier: 3.636A pdb=" N GLU e 65 " --> pdb=" O ASP e 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU e 67 " --> pdb=" O PHE e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 89 removed outlier: 3.788A pdb=" N MET e 73 " --> pdb=" O ARG e 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 34 removed outlier: 3.637A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 86 Processing helix chain 'g' and resid 87 through 93 Processing helix chain 'g' and resid 98 through 106 Processing helix chain 'g' and resid 109 through 111 No H-bonds generated for 'chain 'g' and resid 109 through 111' Processing helix chain 'g' and resid 112 through 131 removed outlier: 3.823A pdb=" N ARG g 117 " --> pdb=" O GLN g 113 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG g 118 " --> pdb=" O GLU g 114 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 93 removed outlier: 3.727A pdb=" N PHE h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU h 68 " --> pdb=" O ASP h 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE h 73 " --> pdb=" O ARG h 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET h 76 " --> pdb=" O LYS h 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR h 78 " --> pdb=" O TYR h 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE h 80 " --> pdb=" O MET h 76 " (cutoff:3.500A) Proline residue: h 81 - end of helix Processing helix chain 'h' and resid 108 through 113 Processing helix chain 'h' and resid 115 through 126 removed outlier: 4.012A pdb=" N ALA h 122 " --> pdb=" O SER h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 164 removed outlier: 4.071A pdb=" N ASN h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG h 161 " --> pdb=" O ARG h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 175 through 179 Processing helix chain 'i' and resid 10 through 27 removed outlier: 3.769A pdb=" N LEU i 15 " --> pdb=" O ARG i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 89 removed outlier: 3.562A pdb=" N HIS i 74 " --> pdb=" O PHE i 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Proline residue: i 78 - end of helix removed outlier: 3.584A pdb=" N PHE i 81 " --> pdb=" O ILE i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 76 removed outlier: 3.602A pdb=" N VAL j 55 " --> pdb=" O THR j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 92 removed outlier: 4.188A pdb=" N TRP j 92 " --> pdb=" O PRO j 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 98 removed outlier: 3.520A pdb=" N LEU j 97 " --> pdb=" O THR j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'k' and resid 33 through 46 removed outlier: 4.162A pdb=" N THR k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 54 removed outlier: 4.268A pdb=" N ARG k 53 " --> pdb=" O PRO k 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 61 removed outlier: 4.336A pdb=" N TYR k 59 " --> pdb=" O GLU k 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY k 61 " --> pdb=" O TRP k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 74 removed outlier: 3.514A pdb=" N VAL k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 90 Processing helix chain 'l' and resid 33 through 37 Processing helix chain 'l' and resid 44 through 55 removed outlier: 3.544A pdb=" N ALA l 52 " --> pdb=" O ARG l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 86 Processing helix chain 'l' and resid 125 through 150 Processing helix chain 'l' and resid 161 through 166 removed outlier: 4.182A pdb=" N ASN l 165 " --> pdb=" O TYR l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 23 Processing helix chain 'm' and resid 26 through 48 removed outlier: 3.991A pdb=" N LEU m 37 " --> pdb=" O GLN m 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER m 38 " --> pdb=" O VAL m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 74 removed outlier: 3.596A pdb=" N ILE m 66 " --> pdb=" O ASP m 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP m 68 " --> pdb=" O ALA m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 Processing helix chain 'm' and resid 95 through 101 Processing helix chain 'm' and resid 101 through 119 removed outlier: 3.810A pdb=" N THR m 107 " --> pdb=" O TYR m 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 18 removed outlier: 3.734A pdb=" N LYS n 15 " --> pdb=" O THR n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 18 through 26 removed outlier: 3.631A pdb=" N ARG n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 50 removed outlier: 3.524A pdb=" N MET n 44 " --> pdb=" O PHE n 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA n 46 " --> pdb=" O CYS n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 74 removed outlier: 3.516A pdb=" N ARG n 65 " --> pdb=" O THR n 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 98 removed outlier: 3.905A pdb=" N CYS n 96 " --> pdb=" O ARG n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 110 through 114 Processing helix chain 'n' and resid 115 through 143 removed outlier: 3.709A pdb=" N PHE n 119 " --> pdb=" O TYR n 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN n 124 " --> pdb=" O SER n 120 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP n 134 " --> pdb=" O MET n 130 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG n 135 " --> pdb=" O GLU n 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 10 removed outlier: 3.763A pdb=" N THR o 6 " --> pdb=" O GLY o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 18 through 22 removed outlier: 3.907A pdb=" N ILE o 22 " --> pdb=" O PRO o 19 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 49 removed outlier: 3.590A pdb=" N MET o 47 " --> pdb=" O GLN o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 56 Processing helix chain 'o' and resid 59 through 72 removed outlier: 3.624A pdb=" N ARG o 65 " --> pdb=" O HIS o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 120 removed outlier: 4.036A pdb=" N LYS o 97 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 41 removed outlier: 3.739A pdb=" N TYR p 32 " --> pdb=" O ASN p 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU p 33 " --> pdb=" O PRO p 29 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU p 39 " --> pdb=" O LYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 59 removed outlier: 4.255A pdb=" N ASN p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 113 removed outlier: 3.524A pdb=" N TRP p 92 " --> pdb=" O ALA p 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE p 102 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET p 103 " --> pdb=" O ASP p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 140 removed outlier: 3.733A pdb=" N GLU p 130 " --> pdb=" O ALA p 126 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN p 131 " --> pdb=" O LYS p 127 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA p 138 " --> pdb=" O LYS p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 174 removed outlier: 3.758A pdb=" N ARG p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU p 164 " --> pdb=" O LYS p 160 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU p 165 " --> pdb=" O GLN p 161 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA p 170 " --> pdb=" O GLU p 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 81 removed outlier: 6.268A pdb=" N MET L 78 " --> pdb=" O HIS L 67 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS L 67 " --> pdb=" O MET L 78 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N PHE L 80 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR L 65 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 440 through 441 Processing sheet with id=AA3, first strand: chain 'O' and resid 84 through 85 removed outlier: 6.208A pdb=" N LYS O 84 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL O 204 " --> pdb=" O LEU O 256 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR O 258 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR O 206 " --> pdb=" O TYR O 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 97 through 98 removed outlier: 5.818A pdb=" N GLU h 97 " --> pdb=" O TYR p 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 1708 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4853 1.25 - 1.40: 8115 1.40 - 1.54: 18924 1.54 - 1.68: 445 1.68 - 1.82: 442 Bond restraints: 32779 Sorted by residual: bond pdb=" O6 EHZ n 201 " pdb=" P1 EHZ n 201 " ideal model delta sigma weight residual 2.378 1.642 0.736 2.00e-02 2.50e+03 1.36e+03 bond pdb=" N PRO O 247 " pdb=" CD PRO O 247 " ideal model delta sigma weight residual 1.473 1.706 -0.233 1.40e-02 5.10e+03 2.77e+02 bond pdb=" N PRO d 115 " pdb=" CD PRO d 115 " ideal model delta sigma weight residual 1.473 1.275 0.198 1.40e-02 5.10e+03 2.00e+02 bond pdb=" N PRO L 265 " pdb=" CD PRO L 265 " ideal model delta sigma weight residual 1.473 1.667 -0.194 1.40e-02 5.10e+03 1.92e+02 bond pdb=" N PRO N 255 " pdb=" CD PRO N 255 " ideal model delta sigma weight residual 1.473 1.282 0.191 1.40e-02 5.10e+03 1.86e+02 ... (remaining 32774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.51: 43664 6.51 - 13.02: 605 13.02 - 19.54: 31 19.54 - 26.05: 1 26.05 - 32.56: 2 Bond angle restraints: 44303 Sorted by residual: angle pdb=" N PRO M 370 " pdb=" CA PRO M 370 " pdb=" C PRO M 370 " ideal model delta sigma weight residual 110.70 128.48 -17.78 1.22e+00 6.72e-01 2.12e+02 angle pdb=" N PRO N 255 " pdb=" CA PRO N 255 " pdb=" C PRO N 255 " ideal model delta sigma weight residual 110.70 128.39 -17.69 1.22e+00 6.72e-01 2.10e+02 angle pdb=" N TYR O 118 " pdb=" CA TYR O 118 " pdb=" C TYR O 118 " ideal model delta sigma weight residual 111.07 125.88 -14.81 1.07e+00 8.73e-01 1.92e+02 angle pdb=" N PRO n 165 " pdb=" CA PRO n 165 " pdb=" C PRO n 165 " ideal model delta sigma weight residual 111.33 130.41 -19.08 1.43e+00 4.89e-01 1.78e+02 angle pdb=" N GLY O 222 " pdb=" CA GLY O 222 " pdb=" C GLY O 222 " ideal model delta sigma weight residual 112.77 129.73 -16.96 1.28e+00 6.10e-01 1.75e+02 ... (remaining 44298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 19522 35.91 - 71.82: 401 71.82 - 107.72: 25 107.72 - 143.63: 8 143.63 - 179.54: 1 Dihedral angle restraints: 19957 sinusoidal: 8700 harmonic: 11257 Sorted by residual: dihedral pdb=" CB CYS p 77 " pdb=" SG CYS p 77 " pdb=" SG CYS p 84 " pdb=" CB CYS p 84 " ideal model delta sinusoidal sigma weight residual -86.00 -160.86 74.86 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS e 43 " pdb=" SG CYS e 43 " pdb=" SG CYS e 56 " pdb=" CB CYS e 56 " ideal model delta sinusoidal sigma weight residual 93.00 160.82 -67.82 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" N LEU d 113 " pdb=" C LEU d 113 " pdb=" CA LEU d 113 " pdb=" CB LEU d 113 " ideal model delta harmonic sigma weight residual 122.80 106.81 15.99 0 2.50e+00 1.60e-01 4.09e+01 ... (remaining 19954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3660 0.105 - 0.210: 900 0.210 - 0.316: 202 0.316 - 0.421: 40 0.421 - 0.526: 13 Chirality restraints: 4815 Sorted by residual: chirality pdb=" CA ASP L 554 " pdb=" N ASP L 554 " pdb=" C ASP L 554 " pdb=" CB ASP L 554 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA LEU d 113 " pdb=" N LEU d 113 " pdb=" C LEU d 113 " pdb=" CB LEU d 113 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA TRP L 557 " pdb=" N TRP L 557 " pdb=" C TRP L 557 " pdb=" CB TRP L 557 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.23e+00 ... (remaining 4812 not shown) Planarity restraints: 5440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR l 112 " 0.025 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C TYR l 112 " -0.083 2.00e-02 2.50e+03 pdb=" O TYR l 112 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE l 113 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS k 19 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C LYS k 19 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS k 19 " -0.028 2.00e-02 2.50e+03 pdb=" N MET k 20 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER l 125 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C SER l 125 " -0.071 2.00e-02 2.50e+03 pdb=" O SER l 125 " 0.027 2.00e-02 2.50e+03 pdb=" N TRP l 126 " 0.023 2.00e-02 2.50e+03 ... (remaining 5437 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 510 2.57 - 3.15: 30808 3.15 - 3.73: 51252 3.73 - 4.32: 75931 4.32 - 4.90: 118497 Nonbonded interactions: 276998 Sorted by model distance: nonbonded pdb=" O ASN l 115 " pdb=" OD1 ASN l 115 " model vdw 1.984 3.040 nonbonded pdb=" O GLU J 76 " pdb=" OE1 GLU J 76 " model vdw 1.990 3.040 nonbonded pdb=" O VAL L 261 " pdb=" CD2 HIS L 264 " model vdw 2.016 3.260 nonbonded pdb=" O ASN L 605 " pdb=" OD1 ASN L 605 " model vdw 2.035 3.040 nonbonded pdb=" NZ LYS L 455 " pdb=" OE1 GLN j 57 " model vdw 2.043 3.120 ... (remaining 276993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.014 0.736 32787 Z= 0.984 Angle : 1.941 42.432 44319 Z= 1.365 Chirality : 0.102 0.526 4815 Planarity : 0.007 0.098 5440 Dihedral : 13.973 179.538 12659 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 44.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 0.32 % Allowed : 5.84 % Favored : 93.84 % Cbeta Deviations : 1.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.12), residues: 3782 helix: -1.20 (0.10), residues: 2385 sheet: -2.21 (1.13), residues: 17 loop : -2.33 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG p 162 TYR 0.035 0.002 TYR l 153 PHE 0.033 0.002 PHE N 35 TRP 0.029 0.002 TRP L 407 HIS 0.008 0.002 HIS l 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01403 / 0.98 (32779) covalent geometry : angle 1.92957 / 1.36 (44303) SS BOND : bond 0.16473 / 11.54 ( 8) SS BOND : angle 11.03210 / 5.63 ( 16) hydrogen bonds : bond 0.22997 / 15.02 ( 1708) hydrogen bonds : angle 8.77154 / 6.37 ( 4950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1414 time to evaluate : 1.256 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: K 95 LEU cc_start: 0.8370 (mt) cc_final: 0.8086 (mp) REVERT: L 287 PHE cc_start: 0.7907 (t80) cc_final: 0.7689 (t80) REVERT: L 559 GLU cc_start: 0.7685 (tt0) cc_final: 0.7476 (tt0) REVERT: M 286 ILE cc_start: 0.8965 (mt) cc_final: 0.8680 (mt) REVERT: M 289 SER cc_start: 0.8629 (t) cc_final: 0.8400 (p) REVERT: M 343 ILE cc_start: 0.8673 (mm) cc_final: 0.8407 (mm) REVERT: N 179 MET cc_start: 0.7974 (mmm) cc_final: 0.7604 (mmt) REVERT: N 221 LEU cc_start: 0.8231 (tp) cc_final: 0.7713 (tt) REVERT: N 237 THR cc_start: 0.8483 (t) cc_final: 0.8201 (p) REVERT: O 66 ILE cc_start: 0.8451 (pp) cc_final: 0.8123 (pp) REVERT: O 235 GLN cc_start: 0.5834 (tp40) cc_final: 0.5433 (tp-100) REVERT: O 261 TRP cc_start: 0.6913 (m-90) cc_final: 0.6642 (m100) REVERT: U 125 GLU cc_start: 0.8280 (tp30) cc_final: 0.8034 (tp30) REVERT: U 155 TYR cc_start: 0.8763 (p90) cc_final: 0.8562 (p90) REVERT: X 162 LYS cc_start: 0.8561 (tptt) cc_final: 0.8346 (tptt) REVERT: Y 115 MET cc_start: 0.7398 (mtm) cc_final: 0.6936 (mtm) REVERT: d 16 ASP cc_start: 0.8138 (p0) cc_final: 0.7925 (p0) REVERT: d 34 MET cc_start: 0.8747 (mmm) cc_final: 0.8429 (mmm) REVERT: d 50 MET cc_start: 0.8464 (mtp) cc_final: 0.8262 (mtm) REVERT: e 27 TYR cc_start: 0.8087 (m-80) cc_final: 0.7719 (m-80) REVERT: e 29 ASN cc_start: 0.8164 (m-40) cc_final: 0.7746 (m-40) REVERT: e 82 GLN cc_start: 0.7703 (tp40) cc_final: 0.7335 (tt0) REVERT: e 83 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7715 (mmt180) REVERT: f 51 ASN cc_start: 0.6884 (m-40) cc_final: 0.6609 (m-40) REVERT: g 81 ASP cc_start: 0.8452 (t0) cc_final: 0.7983 (t70) REVERT: g 135 MET cc_start: 0.9120 (ttm) cc_final: 0.8839 (mtp) REVERT: i 9 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8200 (ttpt) REVERT: i 99 SER cc_start: 0.8963 (p) cc_final: 0.8686 (m) REVERT: i 104 ILE cc_start: 0.9238 (pt) cc_final: 0.8607 (mt) REVERT: i 106 PRO cc_start: 0.8937 (Cg_endo) cc_final: 0.8573 (Cg_endo) REVERT: l 67 ASP cc_start: 0.8496 (t0) cc_final: 0.8257 (t70) REVERT: l 72 TYR cc_start: 0.8718 (m-80) cc_final: 0.8182 (m-80) REVERT: l 74 ASP cc_start: 0.8179 (p0) cc_final: 0.7809 (p0) REVERT: l 108 ASP cc_start: 0.8602 (m-30) cc_final: 0.8367 (m-30) REVERT: l 111 MET cc_start: 0.8602 (ttp) cc_final: 0.8341 (ttm) REVERT: l 165 ASN cc_start: 0.8876 (t0) cc_final: 0.8567 (t0) REVERT: n 9 TYR cc_start: 0.8163 (p90) cc_final: 0.7840 (p90) REVERT: n 74 ASN cc_start: 0.8631 (m110) cc_final: 0.8424 (m-40) REVERT: n 94 TYR cc_start: 0.8737 (m-80) cc_final: 0.8515 (m-80) REVERT: o 43 GLN cc_start: 0.8481 (tt0) cc_final: 0.7898 (tt0) REVERT: o 57 ASP cc_start: 0.5708 (p0) cc_final: 0.5312 (p0) REVERT: o 66 LEU cc_start: 0.9040 (tp) cc_final: 0.8812 (tt) REVERT: p 17 THR cc_start: 0.9184 (m) cc_final: 0.8979 (p) outliers start: 11 outliers final: 1 residues processed: 1417 average time/residue: 0.2189 time to fit residues: 493.7806 Evaluate side-chains 945 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 944 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 3 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 7 ASN L 58 ASN L 175 ASN L 194 ASN ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 321 GLN ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 ASN ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN M 81 GLN M 92 GLN M 168 GLN M 169 ASN M 213 HIS M 304 GLN ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN M 390 ASN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN N 120 GLN N 134 GLN N 172 GLN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 175 ASN ** O 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 HIS Y 12 HIS ** Y 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 91 ASN d 8 HIS e 25 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 HIS f 13 HIS f 39 ASN g 68 ASN h 109 HIS h 170 GLN h 181 HIS i 26 GLN ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 57 GLN ** j 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 91 GLN l 100 ASN l 106 HIS ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 HIS n 33 HIS n 78 GLN o 4 HIS p 67 GLN p 91 GLN p 100 GLN p 124 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112097 restraints weight = 49798.552| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.27 r_work: 0.3273 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32787 Z= 0.195 Angle : 0.792 11.957 44319 Z= 0.406 Chirality : 0.047 0.534 4815 Planarity : 0.006 0.062 5440 Dihedral : 12.989 167.847 5028 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 2.76 % Allowed : 13.99 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3782 helix: 0.21 (0.10), residues: 2429 sheet: -1.76 (1.25), residues: 18 loop : -1.11 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 176 TYR 0.042 0.002 TYR M 406 PHE 0.039 0.002 PHE M 122 TRP 0.017 0.002 TRP L 557 HIS 0.014 0.002 HIS L 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (32779) covalent geometry : angle 0.79058 / 0.41 (44303) SS BOND : bond 0.00407 / 0.25 ( 8) SS BOND : angle 2.37002 / 1.53 ( 16) hydrogen bonds : bond 0.05854 / 3.85 ( 1708) hydrogen bonds : angle 5.24713 / 3.81 ( 4950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1021 time to evaluate : 1.270 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: D 52 MET cc_start: 0.8469 (tpp) cc_final: 0.8242 (mmm) REVERT: J 69 TYR cc_start: 0.8347 (t80) cc_final: 0.8145 (t80) REVERT: J 144 MET cc_start: 0.8587 (mtp) cc_final: 0.7678 (mtm) REVERT: K 21 MET cc_start: 0.8364 (mtm) cc_final: 0.8109 (mtm) REVERT: K 38 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8577 (tt) REVERT: L 61 TYR cc_start: 0.8600 (m-80) cc_final: 0.8396 (m-80) REVERT: L 74 MET cc_start: 0.8753 (ttm) cc_final: 0.8540 (ttm) REVERT: L 79 SER cc_start: 0.9003 (m) cc_final: 0.8763 (p) REVERT: L 199 GLN cc_start: 0.9327 (mp10) cc_final: 0.8673 (mp10) REVERT: L 277 MET cc_start: 0.8754 (ptp) cc_final: 0.8516 (ptp) REVERT: L 366 MET cc_start: 0.8729 (mtp) cc_final: 0.8511 (mtp) REVERT: L 456 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8034 (mtm180) REVERT: L 493 ILE cc_start: 0.8533 (tp) cc_final: 0.8085 (tp) REVERT: L 505 ASN cc_start: 0.8336 (m-40) cc_final: 0.8131 (m-40) REVERT: L 559 GLU cc_start: 0.8553 (tt0) cc_final: 0.8338 (tt0) REVERT: L 589 MET cc_start: 0.8121 (ttm) cc_final: 0.7561 (ttt) REVERT: M 49 TYR cc_start: 0.7770 (m-10) cc_final: 0.7515 (m-10) REVERT: M 77 LEU cc_start: 0.9380 (mt) cc_final: 0.9098 (mt) REVERT: M 135 ARG cc_start: 0.8918 (tpt90) cc_final: 0.8543 (tpt90) REVERT: M 245 ARG cc_start: 0.8504 (mmm160) cc_final: 0.8291 (mmt180) REVERT: M 257 MET cc_start: 0.9036 (tpp) cc_final: 0.8790 (tpp) REVERT: M 316 MET cc_start: 0.8924 (mtm) cc_final: 0.8611 (mtm) REVERT: M 383 MET cc_start: 0.8663 (mtm) cc_final: 0.8443 (mtm) REVERT: M 399 ASN cc_start: 0.8540 (t0) cc_final: 0.8303 (t0) REVERT: M 437 MET cc_start: 0.9082 (mpp) cc_final: 0.8797 (mpp) REVERT: N 43 MET cc_start: 0.8334 (mtp) cc_final: 0.7919 (ttp) REVERT: N 68 MET cc_start: 0.8960 (mmm) cc_final: 0.8743 (mmm) REVERT: N 87 GLN cc_start: 0.7649 (mp10) cc_final: 0.7440 (mp10) REVERT: N 120 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8385 (tp-100) REVERT: N 208 TYR cc_start: 0.8566 (t80) cc_final: 0.7854 (t80) REVERT: N 220 MET cc_start: 0.8179 (ptm) cc_final: 0.7903 (ptm) REVERT: N 276 LEU cc_start: 0.8153 (pp) cc_final: 0.7891 (pp) REVERT: N 313 MET cc_start: 0.7278 (tpp) cc_final: 0.7075 (ttm) REVERT: N 317 GLN cc_start: 0.6862 (mp10) cc_final: 0.6578 (mp10) REVERT: N 335 MET cc_start: 0.8003 (ptp) cc_final: 0.7780 (ptp) REVERT: O 113 SER cc_start: 0.7811 (t) cc_final: 0.7034 (p) REVERT: O 120 ASP cc_start: 0.6860 (t0) cc_final: 0.6214 (t0) REVERT: O 175 ASN cc_start: 0.7778 (m-40) cc_final: 0.7357 (t0) REVERT: O 206 TYR cc_start: 0.5333 (t80) cc_final: 0.4567 (t80) REVERT: O 303 GLU cc_start: 0.7763 (tp30) cc_final: 0.7284 (tp30) REVERT: U 120 MET cc_start: 0.8353 (mtp) cc_final: 0.8037 (mtp) REVERT: X 153 VAL cc_start: 0.9314 (t) cc_final: 0.9113 (p) REVERT: Y 46 ASN cc_start: 0.8663 (t0) cc_final: 0.8399 (t0) REVERT: c 71 ARG cc_start: 0.8432 (mtm110) cc_final: 0.7644 (mtm-85) REVERT: d 34 MET cc_start: 0.9063 (mmm) cc_final: 0.8829 (mmm) REVERT: d 49 ARG cc_start: 0.8464 (mtt180) cc_final: 0.8219 (mtt90) REVERT: d 100 ASP cc_start: 0.8815 (m-30) cc_final: 0.8495 (m-30) REVERT: e 18 PHE cc_start: 0.7865 (p90) cc_final: 0.7594 (p90) REVERT: e 24 GLU cc_start: 0.8204 (tp30) cc_final: 0.7677 (tp30) REVERT: e 37 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6757 (tm-30) REVERT: e 78 ASP cc_start: 0.7916 (m-30) cc_final: 0.7673 (m-30) REVERT: e 82 GLN cc_start: 0.7820 (tp40) cc_final: 0.7026 (tt0) REVERT: e 83 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.6830 (mmt180) REVERT: f 39 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7557 (t0) REVERT: f 47 GLU cc_start: 0.7854 (pm20) cc_final: 0.7626 (pm20) REVERT: g 144 LYS cc_start: 0.9238 (mttm) cc_final: 0.9007 (mttt) REVERT: h 90 ASN cc_start: 0.8821 (m-40) cc_final: 0.8505 (m-40) REVERT: i 101 LYS cc_start: 0.9208 (mttm) cc_final: 0.8826 (mttt) REVERT: i 112 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7917 (mt-10) REVERT: i 123 PHE cc_start: 0.7498 (m-80) cc_final: 0.7294 (m-80) REVERT: i 128 HIS cc_start: 0.6346 (t70) cc_final: 0.5117 (t-170) REVERT: j 43 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: k 39 GLN cc_start: 0.8668 (tp40) cc_final: 0.8087 (tp40) REVERT: l 53 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8692 (ttmm) REVERT: l 91 GLN cc_start: 0.8419 (mm110) cc_final: 0.8191 (mt0) REVERT: l 165 ASN cc_start: 0.9339 (t0) cc_final: 0.9051 (t0) REVERT: l 173 ASP cc_start: 0.8419 (t70) cc_final: 0.8180 (t70) REVERT: l 177 GLU cc_start: 0.7704 (mp0) cc_final: 0.7493 (mp0) REVERT: m 7 LYS cc_start: 0.8344 (tttm) cc_final: 0.8138 (tttm) REVERT: m 31 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8186 (ttt-90) REVERT: n 9 TYR cc_start: 0.8474 (p90) cc_final: 0.8124 (p90) REVERT: n 74 ASN cc_start: 0.8955 (m110) cc_final: 0.8751 (m-40) REVERT: n 90 SER cc_start: 0.9306 (m) cc_final: 0.8933 (t) REVERT: o 44 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7766 (tm-30) REVERT: o 45 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8303 (mt-10) REVERT: o 48 ASP cc_start: 0.8665 (t0) cc_final: 0.8339 (t0) REVERT: o 78 LEU cc_start: 0.8633 (mt) cc_final: 0.8376 (tp) REVERT: p 17 THR cc_start: 0.9111 (m) cc_final: 0.8761 (p) REVERT: p 95 ASP cc_start: 0.8729 (m-30) cc_final: 0.8500 (m-30) REVERT: p 137 LYS cc_start: 0.8436 (tppt) cc_final: 0.8144 (tppt) REVERT: p 161 GLN cc_start: 0.8158 (tt0) cc_final: 0.7828 (tt0) outliers start: 94 outliers final: 44 residues processed: 1066 average time/residue: 0.2057 time to fit residues: 354.5262 Evaluate side-chains 889 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 842 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 285 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain O residue 112 CYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 39 ASN Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 28 LEU Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain j residue 63 SER Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain p residue 53 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 13 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 176 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 299 optimal weight: 0.0070 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 168 GLN M 331 ASN M 415 GLN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN N 204 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN O 235 GLN O 344 ASN Y 19 GLN c 73 ASN d 8 HIS d 59 HIS d 117 HIS e 29 ASN e 98 HIS f 39 ASN g 84 ASN ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 83 HIS l 56 ASN l 80 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 HIS o 54 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108578 restraints weight = 49443.152| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.15 r_work: 0.3221 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32787 Z= 0.173 Angle : 0.685 11.219 44319 Z= 0.348 Chirality : 0.044 0.380 4815 Planarity : 0.005 0.064 5440 Dihedral : 12.517 170.877 5026 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 3.11 % Allowed : 16.08 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3782 helix: 0.62 (0.10), residues: 2443 sheet: -1.63 (1.38), residues: 18 loop : -0.77 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG l 58 TYR 0.034 0.002 TYR M 406 PHE 0.033 0.002 PHE M 122 TRP 0.016 0.001 TRP h 168 HIS 0.011 0.001 HIS d 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (32779) covalent geometry : angle 0.68080 / 0.35 (44303) SS BOND : bond 0.00856 / 0.44 ( 8) SS BOND : angle 3.86623 / 2.19 ( 16) hydrogen bonds : bond 0.05132 / 3.38 ( 1708) hydrogen bonds : angle 4.78993 / 3.47 ( 4950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 884 time to evaluate : 1.156 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: J 135 LEU cc_start: 0.8715 (tt) cc_final: 0.8423 (mt) REVERT: J 144 MET cc_start: 0.8733 (mtp) cc_final: 0.8223 (mtm) REVERT: K 10 MET cc_start: 0.7675 (mmt) cc_final: 0.7328 (mmp) REVERT: K 21 MET cc_start: 0.8619 (mtm) cc_final: 0.8381 (mtm) REVERT: K 38 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8593 (tt) REVERT: L 175 ASN cc_start: 0.8317 (m-40) cc_final: 0.7977 (m-40) REVERT: L 197 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8215 (mm-30) REVERT: L 198 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8720 (mp) REVERT: L 202 MET cc_start: 0.8939 (mtm) cc_final: 0.8402 (mmt) REVERT: L 366 MET cc_start: 0.9095 (mtp) cc_final: 0.8872 (mtp) REVERT: L 401 THR cc_start: 0.9257 (m) cc_final: 0.9003 (p) REVERT: L 424 MET cc_start: 0.9194 (tpp) cc_final: 0.8991 (tpp) REVERT: L 482 MET cc_start: 0.8885 (ptp) cc_final: 0.8673 (ptp) REVERT: L 559 GLU cc_start: 0.8783 (tt0) cc_final: 0.8527 (tt0) REVERT: L 589 MET cc_start: 0.8202 (ttm) cc_final: 0.7600 (ttt) REVERT: L 601 LEU cc_start: 0.8470 (mt) cc_final: 0.7938 (mp) REVERT: M 77 LEU cc_start: 0.9458 (mt) cc_final: 0.9175 (mt) REVERT: M 135 ARG cc_start: 0.9104 (tpt90) cc_final: 0.8844 (tpt90) REVERT: M 200 MET cc_start: 0.8842 (mmt) cc_final: 0.8573 (mmm) REVERT: M 245 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8289 (mmt180) REVERT: M 257 MET cc_start: 0.9143 (tpp) cc_final: 0.8893 (tpp) REVERT: M 271 MET cc_start: 0.8212 (mmm) cc_final: 0.7716 (mtp) REVERT: M 423 MET cc_start: 0.7179 (mmt) cc_final: 0.5991 (mmt) REVERT: N 2 ASN cc_start: 0.7663 (m110) cc_final: 0.7369 (m110) REVERT: N 68 MET cc_start: 0.9114 (mmm) cc_final: 0.8787 (mmm) REVERT: N 87 GLN cc_start: 0.8079 (mp10) cc_final: 0.7785 (mm-40) REVERT: N 208 TYR cc_start: 0.8799 (t80) cc_final: 0.8137 (t80) REVERT: N 220 MET cc_start: 0.8278 (ptm) cc_final: 0.7921 (ptm) REVERT: N 240 MET cc_start: 0.8151 (mtm) cc_final: 0.7721 (ptp) REVERT: N 276 LEU cc_start: 0.8095 (pp) cc_final: 0.7868 (pp) REVERT: N 313 MET cc_start: 0.7366 (tpp) cc_final: 0.6829 (ttm) REVERT: N 317 GLN cc_start: 0.7000 (mp10) cc_final: 0.6478 (mp10) REVERT: O 55 GLU cc_start: 0.6148 (pp20) cc_final: 0.5674 (pp20) REVERT: O 113 SER cc_start: 0.7979 (t) cc_final: 0.7601 (p) REVERT: O 120 ASP cc_start: 0.7008 (t0) cc_final: 0.6327 (t0) REVERT: O 180 ARG cc_start: 0.5406 (mtm-85) cc_final: 0.4779 (mtm180) REVERT: O 182 GLN cc_start: 0.9094 (mp10) cc_final: 0.8689 (mp10) REVERT: O 255 VAL cc_start: 0.8422 (t) cc_final: 0.8156 (p) REVERT: O 289 TRP cc_start: 0.7457 (m100) cc_final: 0.7246 (m100) REVERT: O 303 GLU cc_start: 0.7928 (tp30) cc_final: 0.7460 (tp30) REVERT: O 314 LEU cc_start: 0.7630 (tp) cc_final: 0.6968 (tp) REVERT: U 130 ILE cc_start: 0.8234 (mm) cc_final: 0.8023 (mm) REVERT: U 152 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8827 (mmtm) REVERT: Y 46 ASN cc_start: 0.8870 (t0) cc_final: 0.8434 (t0) REVERT: d 34 MET cc_start: 0.9170 (mmm) cc_final: 0.8952 (mmm) REVERT: d 49 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8400 (mtt90) REVERT: e 18 PHE cc_start: 0.8145 (p90) cc_final: 0.7912 (p90) REVERT: e 37 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7037 (tm-30) REVERT: e 78 ASP cc_start: 0.8262 (m-30) cc_final: 0.8032 (m-30) REVERT: e 82 GLN cc_start: 0.7854 (tp40) cc_final: 0.7150 (tt0) REVERT: e 83 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7011 (mmt180) REVERT: f 47 GLU cc_start: 0.8238 (pm20) cc_final: 0.7883 (pm20) REVERT: g 62 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: g 77 ASP cc_start: 0.8444 (p0) cc_final: 0.8232 (p0) REVERT: g 114 GLU cc_start: 0.8594 (tp30) cc_final: 0.8334 (tp30) REVERT: g 144 LYS cc_start: 0.9367 (mttm) cc_final: 0.8978 (mtpt) REVERT: h 76 MET cc_start: 0.8442 (ttp) cc_final: 0.8230 (ttp) REVERT: h 90 ASN cc_start: 0.9028 (m-40) cc_final: 0.8563 (m110) REVERT: i 27 GLU cc_start: 0.8753 (tt0) cc_final: 0.8532 (tt0) REVERT: i 101 LYS cc_start: 0.9185 (mttm) cc_final: 0.8829 (mttt) REVERT: i 112 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8144 (mt-10) REVERT: i 128 HIS cc_start: 0.6381 (t70) cc_final: 0.5266 (t-170) REVERT: j 43 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8653 (mmm-85) REVERT: j 52 ARG cc_start: 0.8933 (tpp80) cc_final: 0.8708 (mmm160) REVERT: j 88 ASP cc_start: 0.9102 (t0) cc_final: 0.8882 (t0) REVERT: k 39 GLN cc_start: 0.8612 (tp40) cc_final: 0.8300 (tp-100) REVERT: k 49 ASP cc_start: 0.6874 (t0) cc_final: 0.6394 (t0) REVERT: k 59 TYR cc_start: 0.9347 (m-80) cc_final: 0.9108 (m-80) REVERT: l 36 MET cc_start: 0.8018 (ttm) cc_final: 0.7663 (ttm) REVERT: l 165 ASN cc_start: 0.9400 (t0) cc_final: 0.9038 (t0) REVERT: l 177 GLU cc_start: 0.8008 (mp0) cc_final: 0.7749 (mp0) REVERT: m 62 ASP cc_start: 0.8340 (t0) cc_final: 0.8112 (t0) REVERT: n 9 TYR cc_start: 0.8599 (p90) cc_final: 0.8160 (p90) REVERT: n 73 GLN cc_start: 0.8943 (tt0) cc_final: 0.8533 (mt0) REVERT: n 90 SER cc_start: 0.9268 (m) cc_final: 0.8965 (t) REVERT: n 124 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8400 (mm-40) REVERT: o 36 GLU cc_start: 0.8841 (pm20) cc_final: 0.8640 (pm20) REVERT: o 44 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8307 (tm-30) REVERT: o 45 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8398 (mt-10) REVERT: o 48 ASP cc_start: 0.8715 (t0) cc_final: 0.8429 (t0) REVERT: p 17 THR cc_start: 0.9148 (m) cc_final: 0.8834 (p) REVERT: p 137 LYS cc_start: 0.8464 (tppt) cc_final: 0.8057 (tppt) REVERT: p 161 GLN cc_start: 0.8339 (tt0) cc_final: 0.8065 (tt0) outliers start: 106 outliers final: 60 residues processed: 931 average time/residue: 0.1913 time to fit residues: 291.5136 Evaluate side-chains 876 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 813 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 369 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 285 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 344 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 29 ASN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 93 THR Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 113 ILE Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 5 TRP Chi-restraints excluded: chain p residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 305 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 292 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** M 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN N 222 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 HIS O 344 ASN d 8 HIS d 97 HIS ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 172 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106228 restraints weight = 49238.020| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.16 r_work: 0.3182 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32787 Z= 0.177 Angle : 0.661 10.935 44319 Z= 0.333 Chirality : 0.044 0.339 4815 Planarity : 0.005 0.065 5440 Dihedral : 12.314 170.168 5026 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 3.37 % Allowed : 17.16 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3782 helix: 0.80 (0.11), residues: 2438 sheet: -1.38 (1.53), residues: 18 loop : -0.62 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 71 TYR 0.026 0.002 TYR M 406 PHE 0.031 0.002 PHE M 122 TRP 0.015 0.001 TRP p 5 HIS 0.011 0.001 HIS d 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (32779) covalent geometry : angle 0.65873 / 0.33 (44303) SS BOND : bond 0.01518 / 1.18 ( 8) SS BOND : angle 2.65830 / 1.50 ( 16) hydrogen bonds : bond 0.04708 / 3.10 ( 1708) hydrogen bonds : angle 4.61724 / 3.34 ( 4950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 871 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 35 SER cc_start: 0.9293 (m) cc_final: 0.8836 (p) REVERT: J 135 LEU cc_start: 0.8618 (tt) cc_final: 0.8339 (mt) REVERT: J 144 MET cc_start: 0.8790 (mtp) cc_final: 0.8304 (mtm) REVERT: K 10 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7476 (mmp) REVERT: K 21 MET cc_start: 0.8642 (mtm) cc_final: 0.8402 (mtm) REVERT: K 50 ASN cc_start: 0.8979 (p0) cc_final: 0.8760 (p0) REVERT: L 175 ASN cc_start: 0.8470 (m-40) cc_final: 0.8175 (m-40) REVERT: L 198 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8765 (mp) REVERT: L 202 MET cc_start: 0.8889 (mtm) cc_final: 0.8479 (mmt) REVERT: L 401 THR cc_start: 0.9225 (m) cc_final: 0.8955 (p) REVERT: L 424 MET cc_start: 0.9254 (tpp) cc_final: 0.8950 (tpp) REVERT: L 507 LEU cc_start: 0.8709 (mp) cc_final: 0.8486 (mp) REVERT: L 559 GLU cc_start: 0.8914 (tt0) cc_final: 0.8546 (tt0) REVERT: L 589 MET cc_start: 0.8181 (ttm) cc_final: 0.7544 (ttt) REVERT: M 77 LEU cc_start: 0.9460 (mt) cc_final: 0.9101 (mt) REVERT: M 95 TYR cc_start: 0.8818 (t80) cc_final: 0.8023 (t80) REVERT: M 200 MET cc_start: 0.8931 (mmt) cc_final: 0.8706 (mmm) REVERT: M 396 MET cc_start: 0.8605 (tpt) cc_final: 0.8347 (mmm) REVERT: M 423 MET cc_start: 0.7124 (mmt) cc_final: 0.5971 (mmt) REVERT: N 43 MET cc_start: 0.8738 (mmm) cc_final: 0.8447 (tpt) REVERT: N 68 MET cc_start: 0.9186 (mmm) cc_final: 0.8859 (mmm) REVERT: N 87 GLN cc_start: 0.8383 (mp10) cc_final: 0.8064 (mm-40) REVERT: N 126 MET cc_start: 0.7138 (mmt) cc_final: 0.6760 (mmp) REVERT: N 134 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8843 (mm-40) REVERT: N 208 TYR cc_start: 0.8864 (t80) cc_final: 0.8258 (t80) REVERT: N 220 MET cc_start: 0.8318 (ptm) cc_final: 0.7950 (ptm) REVERT: N 276 LEU cc_start: 0.8135 (pp) cc_final: 0.7902 (pp) REVERT: N 313 MET cc_start: 0.7587 (tpp) cc_final: 0.7172 (ttm) REVERT: N 317 GLN cc_start: 0.6905 (mp10) cc_final: 0.6294 (mp10) REVERT: O 55 GLU cc_start: 0.6242 (pp20) cc_final: 0.5781 (pp20) REVERT: O 113 SER cc_start: 0.8228 (t) cc_final: 0.7859 (p) REVERT: O 116 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7242 (tttm) REVERT: O 120 ASP cc_start: 0.7037 (t0) cc_final: 0.6663 (t0) REVERT: O 123 SER cc_start: 0.8144 (m) cc_final: 0.7867 (t) REVERT: O 125 ASP cc_start: 0.8316 (p0) cc_final: 0.7956 (p0) REVERT: O 182 GLN cc_start: 0.9103 (mp10) cc_final: 0.8735 (mp10) REVERT: O 185 ASP cc_start: 0.8886 (m-30) cc_final: 0.8661 (m-30) REVERT: O 227 MET cc_start: 0.6822 (mtt) cc_final: 0.6585 (ptp) REVERT: O 303 GLU cc_start: 0.7974 (tp30) cc_final: 0.7386 (tp30) REVERT: O 351 TRP cc_start: 0.7985 (m100) cc_final: 0.7533 (m-90) REVERT: X 170 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.7607 (m-90) REVERT: Y 46 ASN cc_start: 0.8940 (t0) cc_final: 0.8510 (t0) REVERT: c 71 ARG cc_start: 0.8752 (mtm110) cc_final: 0.8490 (mtm-85) REVERT: d 1 MET cc_start: 0.6652 (tpt) cc_final: 0.5863 (tpt) REVERT: d 49 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8302 (mtt90) REVERT: e 18 PHE cc_start: 0.8404 (p90) cc_final: 0.8028 (p90) REVERT: e 37 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7087 (tm-30) REVERT: e 78 ASP cc_start: 0.8329 (m-30) cc_final: 0.8066 (m-30) REVERT: e 82 GLN cc_start: 0.7892 (tp40) cc_final: 0.7180 (tt0) REVERT: e 83 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.6964 (mmt180) REVERT: e 87 MET cc_start: 0.8882 (ttm) cc_final: 0.8443 (mmt) REVERT: f 47 GLU cc_start: 0.8243 (pm20) cc_final: 0.7943 (pm20) REVERT: g 62 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: g 113 GLN cc_start: 0.8564 (pt0) cc_final: 0.8360 (mt0) REVERT: g 144 LYS cc_start: 0.9411 (mttm) cc_final: 0.9176 (mttt) REVERT: h 90 ASN cc_start: 0.9047 (m-40) cc_final: 0.8596 (m110) REVERT: i 13 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8253 (mt0) REVERT: i 27 GLU cc_start: 0.8747 (tt0) cc_final: 0.8476 (tt0) REVERT: i 87 LYS cc_start: 0.9335 (tttt) cc_final: 0.8895 (tttm) REVERT: i 101 LYS cc_start: 0.9176 (mttm) cc_final: 0.8826 (mttt) REVERT: i 112 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8304 (mt-10) REVERT: i 128 HIS cc_start: 0.6544 (t70) cc_final: 0.5523 (t70) REVERT: j 43 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8582 (mmm-85) REVERT: j 88 ASP cc_start: 0.9092 (t0) cc_final: 0.8885 (t0) REVERT: j 96 GLU cc_start: 0.8694 (tp30) cc_final: 0.8462 (tp30) REVERT: k 49 ASP cc_start: 0.7111 (t0) cc_final: 0.6479 (t70) REVERT: l 36 MET cc_start: 0.8364 (ttm) cc_final: 0.8145 (ttm) REVERT: l 122 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8416 (p) REVERT: l 165 ASN cc_start: 0.9405 (t0) cc_final: 0.9081 (t0) REVERT: l 173 ASP cc_start: 0.8506 (t70) cc_final: 0.8240 (t70) REVERT: l 177 GLU cc_start: 0.8074 (mp0) cc_final: 0.7839 (mp0) REVERT: m 31 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8215 (ttt-90) REVERT: m 62 ASP cc_start: 0.8403 (t0) cc_final: 0.8176 (t0) REVERT: n 90 SER cc_start: 0.9295 (m) cc_final: 0.9024 (t) REVERT: n 124 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8353 (mm-40) REVERT: o 36 GLU cc_start: 0.8842 (pm20) cc_final: 0.8574 (pm20) REVERT: o 44 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8468 (tm-30) REVERT: o 48 ASP cc_start: 0.8766 (t0) cc_final: 0.8448 (t0) REVERT: p 17 THR cc_start: 0.9121 (m) cc_final: 0.8754 (p) REVERT: p 73 ASP cc_start: 0.8243 (p0) cc_final: 0.7974 (p0) REVERT: p 114 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8265 (tm-30) REVERT: p 137 LYS cc_start: 0.8511 (tppt) cc_final: 0.8026 (tppt) outliers start: 115 outliers final: 67 residues processed: 925 average time/residue: 0.1957 time to fit residues: 295.4979 Evaluate side-chains 893 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 821 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain L residue 597 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 112 CYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 218 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 170 TRP Chi-restraints excluded: chain X residue 171 THR Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 112 ILE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 93 THR Chi-restraints excluded: chain e residue 98 HIS Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain l residue 82 SER Chi-restraints excluded: chain l residue 113 ILE Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 122 THR Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 5 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 9 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 427 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 HIS h 132 ASN ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN o 54 GLN p 107 GLN p 124 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104142 restraints weight = 48839.827| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.22 r_work: 0.3155 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32787 Z= 0.151 Angle : 0.636 13.221 44319 Z= 0.317 Chirality : 0.043 0.333 4815 Planarity : 0.005 0.065 5440 Dihedral : 12.149 171.690 5026 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 3.46 % Allowed : 17.28 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3782 helix: 0.94 (0.11), residues: 2442 sheet: -1.32 (1.50), residues: 18 loop : -0.57 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 71 TYR 0.026 0.001 TYR M 406 PHE 0.030 0.002 PHE M 122 TRP 0.013 0.001 TRP p 5 HIS 0.011 0.001 HIS d 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (32779) covalent geometry : angle 0.63462 / 0.32 (44303) SS BOND : bond 0.00478 / 0.36 ( 8) SS BOND : angle 2.21953 / 1.27 ( 16) hydrogen bonds : bond 0.04455 / 2.93 ( 1708) hydrogen bonds : angle 4.49241 / 3.25 ( 4950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 880 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 144 MET cc_start: 0.8790 (mtp) cc_final: 0.8330 (mtm) REVERT: K 10 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7510 (mmp) REVERT: K 21 MET cc_start: 0.8659 (mtm) cc_final: 0.8428 (mtm) REVERT: K 50 ASN cc_start: 0.8959 (p0) cc_final: 0.8717 (p0) REVERT: L 82 THR cc_start: 0.8372 (p) cc_final: 0.8115 (p) REVERT: L 128 MET cc_start: 0.9046 (tpt) cc_final: 0.8788 (tpt) REVERT: L 175 ASN cc_start: 0.8501 (m-40) cc_final: 0.8209 (m-40) REVERT: L 198 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8538 (mp) REVERT: L 214 MET cc_start: 0.8611 (tpt) cc_final: 0.8324 (tpt) REVERT: L 401 THR cc_start: 0.9192 (m) cc_final: 0.8904 (p) REVERT: L 424 MET cc_start: 0.9234 (tpp) cc_final: 0.9026 (tpp) REVERT: L 479 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8619 (p) REVERT: L 585 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8029 (mtpp) REVERT: L 589 MET cc_start: 0.8173 (ttm) cc_final: 0.7561 (ttt) REVERT: M 77 LEU cc_start: 0.9431 (mt) cc_final: 0.9140 (mt) REVERT: M 95 TYR cc_start: 0.8834 (t80) cc_final: 0.8024 (t80) REVERT: M 200 MET cc_start: 0.8912 (mmt) cc_final: 0.8601 (mmm) REVERT: M 271 MET cc_start: 0.8206 (mmm) cc_final: 0.7763 (mtp) REVERT: M 399 ASN cc_start: 0.8737 (t0) cc_final: 0.8421 (t0) REVERT: M 437 MET cc_start: 0.9254 (mpp) cc_final: 0.8799 (mmt) REVERT: N 43 MET cc_start: 0.8734 (mmm) cc_final: 0.8405 (tpt) REVERT: N 68 MET cc_start: 0.9157 (mmm) cc_final: 0.8790 (mmm) REVERT: N 79 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8424 (tptm) REVERT: N 87 GLN cc_start: 0.8499 (mp10) cc_final: 0.8038 (mm-40) REVERT: N 126 MET cc_start: 0.7126 (mmt) cc_final: 0.6615 (mmp) REVERT: N 208 TYR cc_start: 0.8861 (t80) cc_final: 0.8308 (t80) REVERT: N 220 MET cc_start: 0.8315 (ptm) cc_final: 0.7924 (ptm) REVERT: N 276 LEU cc_start: 0.8138 (pp) cc_final: 0.7843 (pp) REVERT: N 287 LEU cc_start: 0.9318 (tp) cc_final: 0.9097 (tp) REVERT: N 313 MET cc_start: 0.7473 (tpp) cc_final: 0.6950 (ttm) REVERT: N 317 GLN cc_start: 0.6730 (mp10) cc_final: 0.6067 (mp10) REVERT: O 55 GLU cc_start: 0.6193 (pp20) cc_final: 0.5685 (tm-30) REVERT: O 113 SER cc_start: 0.8229 (t) cc_final: 0.7840 (p) REVERT: O 116 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7254 (tttm) REVERT: O 120 ASP cc_start: 0.7258 (t0) cc_final: 0.6940 (t0) REVERT: O 123 SER cc_start: 0.8183 (m) cc_final: 0.7869 (t) REVERT: O 125 ASP cc_start: 0.8370 (p0) cc_final: 0.7828 (p0) REVERT: O 182 GLN cc_start: 0.9033 (mp10) cc_final: 0.8703 (mp10) REVERT: O 185 ASP cc_start: 0.8822 (m-30) cc_final: 0.8483 (m-30) REVERT: O 249 MET cc_start: 0.5578 (mmm) cc_final: 0.5299 (mmm) REVERT: O 276 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7328 (pp) REVERT: O 303 GLU cc_start: 0.8023 (tp30) cc_final: 0.7646 (tp30) REVERT: O 343 TYR cc_start: 0.9111 (m-80) cc_final: 0.8805 (m-80) REVERT: Y 46 ASN cc_start: 0.8925 (t0) cc_final: 0.8513 (t0) REVERT: c 47 SER cc_start: 0.8351 (m) cc_final: 0.8034 (p) REVERT: c 71 ARG cc_start: 0.8745 (mtm110) cc_final: 0.8503 (mtm-85) REVERT: d 1 MET cc_start: 0.6452 (tpt) cc_final: 0.5559 (tpt) REVERT: d 49 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8345 (mtt90) REVERT: e 18 PHE cc_start: 0.8611 (p90) cc_final: 0.8244 (p90) REVERT: e 78 ASP cc_start: 0.8332 (m-30) cc_final: 0.8069 (m-30) REVERT: e 82 GLN cc_start: 0.7833 (tp40) cc_final: 0.7171 (tt0) REVERT: e 83 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6875 (mmt180) REVERT: e 87 MET cc_start: 0.8926 (ttm) cc_final: 0.8468 (mmt) REVERT: g 62 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: g 81 ASP cc_start: 0.8947 (t70) cc_final: 0.8139 (t0) REVERT: g 144 LYS cc_start: 0.9335 (mttm) cc_final: 0.8920 (mtpt) REVERT: h 90 ASN cc_start: 0.9051 (m-40) cc_final: 0.8603 (m110) REVERT: h 160 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8718 (ttm) REVERT: i 27 GLU cc_start: 0.8661 (tt0) cc_final: 0.8245 (tt0) REVERT: i 87 LYS cc_start: 0.9356 (tttt) cc_final: 0.8896 (tttm) REVERT: i 101 LYS cc_start: 0.9077 (mttm) cc_final: 0.8715 (mttt) REVERT: i 128 HIS cc_start: 0.6418 (t70) cc_final: 0.5364 (t70) REVERT: j 43 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: j 52 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8354 (tpp80) REVERT: j 88 ASP cc_start: 0.9102 (t0) cc_final: 0.8893 (t0) REVERT: j 96 GLU cc_start: 0.8685 (tp30) cc_final: 0.8429 (tp30) REVERT: k 49 ASP cc_start: 0.7496 (t0) cc_final: 0.6674 (t0) REVERT: l 36 MET cc_start: 0.8577 (ttm) cc_final: 0.8327 (ttp) REVERT: l 53 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8838 (tttm) REVERT: l 122 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8400 (p) REVERT: l 165 ASN cc_start: 0.9433 (t0) cc_final: 0.9093 (t0) REVERT: l 173 ASP cc_start: 0.8524 (t70) cc_final: 0.8226 (t70) REVERT: l 177 GLU cc_start: 0.8080 (mp0) cc_final: 0.7841 (mp0) REVERT: l 186 ILE cc_start: 0.7811 (mt) cc_final: 0.7214 (mm) REVERT: m 62 ASP cc_start: 0.8490 (t0) cc_final: 0.8197 (t0) REVERT: n 90 SER cc_start: 0.9247 (m) cc_final: 0.9042 (t) REVERT: n 124 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8390 (mm-40) REVERT: o 36 GLU cc_start: 0.8898 (pm20) cc_final: 0.8581 (pm20) REVERT: o 44 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8556 (tm-30) REVERT: o 48 ASP cc_start: 0.8782 (t0) cc_final: 0.8576 (t0) REVERT: p 17 THR cc_start: 0.9039 (m) cc_final: 0.8808 (t) REVERT: p 73 ASP cc_start: 0.8188 (p0) cc_final: 0.7751 (p0) REVERT: p 81 ASP cc_start: 0.8260 (t0) cc_final: 0.7718 (t0) REVERT: p 137 LYS cc_start: 0.8467 (tppt) cc_final: 0.8121 (tppt) outliers start: 118 outliers final: 67 residues processed: 940 average time/residue: 0.2000 time to fit residues: 307.2192 Evaluate side-chains 896 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 821 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 565 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 276 LEU Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain e residue 93 THR Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 95 GLU Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 122 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 5 TRP Chi-restraints excluded: chain p residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 314 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 206 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 170 GLN L 192 ASN ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN M 89 ASN ** M 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN M 422 HIS N 134 GLN N 172 GLN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN d 8 HIS h 132 ASN i 74 HIS l 84 HIS ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103693 restraints weight = 48680.155| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3149 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32787 Z= 0.149 Angle : 0.651 13.608 44319 Z= 0.322 Chirality : 0.043 0.301 4815 Planarity : 0.005 0.066 5440 Dihedral : 12.024 171.181 5026 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 3.61 % Allowed : 18.07 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3782 helix: 1.04 (0.11), residues: 2445 sheet: -1.35 (1.49), residues: 18 loop : -0.46 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 81 TYR 0.025 0.001 TYR J 69 PHE 0.027 0.001 PHE M 122 TRP 0.015 0.001 TRP X 170 HIS 0.010 0.001 HIS d 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (32779) covalent geometry : angle 0.64742 / 0.32 (44303) SS BOND : bond 0.00471 / 0.23 ( 8) SS BOND : angle 3.75692 / 2.07 ( 16) hydrogen bonds : bond 0.04308 / 2.83 ( 1708) hydrogen bonds : angle 4.45068 / 3.23 ( 4950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 853 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 54 MET cc_start: 0.8606 (tmm) cc_final: 0.8214 (tmm) REVERT: J 144 MET cc_start: 0.8796 (mtp) cc_final: 0.8285 (mtp) REVERT: J 171 ARG cc_start: 0.7639 (tmm-80) cc_final: 0.7319 (tmm-80) REVERT: K 21 MET cc_start: 0.8688 (mtm) cc_final: 0.8448 (mtm) REVERT: K 31 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8614 (mm) REVERT: K 50 ASN cc_start: 0.8935 (p0) cc_final: 0.8688 (p0) REVERT: L 128 MET cc_start: 0.9002 (tpt) cc_final: 0.8763 (tpt) REVERT: L 175 ASN cc_start: 0.8417 (m-40) cc_final: 0.8146 (m-40) REVERT: L 198 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8654 (mp) REVERT: L 401 THR cc_start: 0.9173 (m) cc_final: 0.8879 (p) REVERT: L 424 MET cc_start: 0.9258 (tpp) cc_final: 0.8995 (tpp) REVERT: L 585 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8023 (mtpp) REVERT: L 589 MET cc_start: 0.8179 (ttm) cc_final: 0.7560 (ttt) REVERT: M 77 LEU cc_start: 0.9482 (mt) cc_final: 0.9203 (mt) REVERT: M 95 TYR cc_start: 0.8878 (t80) cc_final: 0.8140 (t80) REVERT: M 200 MET cc_start: 0.8914 (mmt) cc_final: 0.8608 (mmm) REVERT: M 271 MET cc_start: 0.8232 (mmm) cc_final: 0.7865 (mtp) REVERT: M 423 MET cc_start: 0.7071 (mmt) cc_final: 0.6098 (mmt) REVERT: M 437 MET cc_start: 0.9260 (mpp) cc_final: 0.8809 (mmt) REVERT: N 36 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8516 (p) REVERT: N 43 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8456 (tpt) REVERT: N 68 MET cc_start: 0.9197 (mmm) cc_final: 0.8851 (mmm) REVERT: N 87 GLN cc_start: 0.8580 (mp10) cc_final: 0.8269 (mm-40) REVERT: N 126 MET cc_start: 0.7134 (mmt) cc_final: 0.6691 (mmp) REVERT: N 220 MET cc_start: 0.8321 (ptm) cc_final: 0.7936 (ptm) REVERT: N 271 MET cc_start: 0.9313 (mmm) cc_final: 0.8980 (mmm) REVERT: N 276 LEU cc_start: 0.8072 (pp) cc_final: 0.7660 (pp) REVERT: N 313 MET cc_start: 0.7451 (tpp) cc_final: 0.6949 (ttm) REVERT: N 317 GLN cc_start: 0.6707 (mp10) cc_final: 0.6037 (mp10) REVERT: O 55 GLU cc_start: 0.6232 (pp20) cc_final: 0.5729 (tm-30) REVERT: O 113 SER cc_start: 0.8277 (t) cc_final: 0.7816 (p) REVERT: O 116 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7311 (tttm) REVERT: O 120 ASP cc_start: 0.7198 (t0) cc_final: 0.6918 (t0) REVERT: O 123 SER cc_start: 0.8112 (m) cc_final: 0.7906 (t) REVERT: O 125 ASP cc_start: 0.8485 (p0) cc_final: 0.7965 (p0) REVERT: O 182 GLN cc_start: 0.9101 (mp10) cc_final: 0.8761 (mp10) REVERT: O 185 ASP cc_start: 0.8791 (m-30) cc_final: 0.8519 (m-30) REVERT: O 235 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7480 (tp-100) REVERT: O 239 ASN cc_start: 0.7553 (m110) cc_final: 0.7108 (m110) REVERT: O 249 MET cc_start: 0.5619 (mmm) cc_final: 0.5395 (mmm) REVERT: O 283 TRP cc_start: 0.7606 (m100) cc_final: 0.7312 (m100) REVERT: O 303 GLU cc_start: 0.7918 (tp30) cc_final: 0.7340 (tp30) REVERT: U 155 TYR cc_start: 0.9256 (p90) cc_final: 0.8679 (p90) REVERT: Y 46 ASN cc_start: 0.8886 (t0) cc_final: 0.8534 (t0) REVERT: c 47 SER cc_start: 0.8281 (m) cc_final: 0.7960 (p) REVERT: d 1 MET cc_start: 0.6397 (tpt) cc_final: 0.5466 (tpt) REVERT: e 5 ASP cc_start: 0.8271 (t0) cc_final: 0.7971 (t70) REVERT: e 82 GLN cc_start: 0.7858 (tp40) cc_final: 0.7177 (tt0) REVERT: e 83 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6820 (mmt180) REVERT: e 87 MET cc_start: 0.8944 (ttm) cc_final: 0.8519 (mmt) REVERT: g 62 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: g 81 ASP cc_start: 0.8964 (t70) cc_final: 0.8314 (t0) REVERT: g 144 LYS cc_start: 0.9333 (mttm) cc_final: 0.9083 (mttt) REVERT: h 90 ASN cc_start: 0.9045 (m-40) cc_final: 0.8598 (m110) REVERT: i 27 GLU cc_start: 0.8655 (tt0) cc_final: 0.8218 (tt0) REVERT: i 87 LYS cc_start: 0.9351 (tttt) cc_final: 0.8911 (tttm) REVERT: i 93 LYS cc_start: 0.8681 (mttm) cc_final: 0.8320 (mmtp) REVERT: i 101 LYS cc_start: 0.9048 (mttm) cc_final: 0.8675 (mttt) REVERT: i 112 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7621 (mt-10) REVERT: i 128 HIS cc_start: 0.6468 (t70) cc_final: 0.5379 (t70) REVERT: j 52 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8365 (tpp80) REVERT: j 88 ASP cc_start: 0.9112 (t0) cc_final: 0.8842 (t0) REVERT: j 96 GLU cc_start: 0.8710 (tp30) cc_final: 0.8499 (tp30) REVERT: k 36 GLU cc_start: 0.8168 (tt0) cc_final: 0.7852 (mt-10) REVERT: k 60 MET cc_start: 0.8907 (tpp) cc_final: 0.8260 (mmm) REVERT: l 53 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8821 (tttm) REVERT: l 81 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8263 (mmm-85) REVERT: l 122 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8431 (p) REVERT: l 165 ASN cc_start: 0.9446 (t0) cc_final: 0.9104 (t0) REVERT: l 173 ASP cc_start: 0.8573 (t70) cc_final: 0.8258 (t70) REVERT: l 177 GLU cc_start: 0.8102 (mp0) cc_final: 0.7883 (mp0) REVERT: l 186 ILE cc_start: 0.7884 (mt) cc_final: 0.7324 (mm) REVERT: m 7 LYS cc_start: 0.8677 (tttm) cc_final: 0.8475 (ttpp) REVERT: m 31 ARG cc_start: 0.8618 (ttm110) cc_final: 0.8013 (ttt-90) REVERT: m 62 ASP cc_start: 0.8587 (t0) cc_final: 0.8287 (t0) REVERT: n 124 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8395 (mm-40) REVERT: o 36 GLU cc_start: 0.8907 (pm20) cc_final: 0.8682 (pm20) REVERT: o 44 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8602 (tm-30) REVERT: p 15 SER cc_start: 0.8695 (m) cc_final: 0.7682 (p) REVERT: p 73 ASP cc_start: 0.8298 (p0) cc_final: 0.8082 (p0) REVERT: p 81 ASP cc_start: 0.8100 (t0) cc_final: 0.7709 (t70) REVERT: p 114 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8444 (tm-30) REVERT: p 137 LYS cc_start: 0.8578 (tppt) cc_final: 0.8099 (tppt) outliers start: 123 outliers final: 79 residues processed: 912 average time/residue: 0.1852 time to fit residues: 275.2070 Evaluate side-chains 887 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 801 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 285 MET Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain X residue 171 THR Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain e residue 98 HIS Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 122 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain l residue 175 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 80 CYS Chi-restraints excluded: chain o residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 245 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 69 optimal weight: 0.2980 chunk 174 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 186 HIS ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 HIS j 54 GLN ** j 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 80 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098624 restraints weight = 49144.883| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.21 r_work: 0.3071 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 32787 Z= 0.243 Angle : 0.725 18.082 44319 Z= 0.359 Chirality : 0.046 0.304 4815 Planarity : 0.005 0.064 5440 Dihedral : 12.115 166.701 5026 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 3.87 % Allowed : 18.57 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3782 helix: 0.97 (0.10), residues: 2453 sheet: -1.30 (1.47), residues: 18 loop : -0.55 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 49 TYR 0.025 0.002 TYR J 69 PHE 0.029 0.002 PHE M 380 TRP 0.020 0.002 TRP h 168 HIS 0.005 0.001 HIS M 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (32779) covalent geometry : angle 0.72155 / 0.36 (44303) SS BOND : bond 0.00313 / 0.20 ( 8) SS BOND : angle 3.58995 / 1.94 ( 16) hydrogen bonds : bond 0.04674 / 3.08 ( 1708) hydrogen bonds : angle 4.55421 / 3.30 ( 4950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 812 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 144 MET cc_start: 0.8853 (mtp) cc_final: 0.8382 (mtp) REVERT: J 171 ARG cc_start: 0.7700 (tmm-80) cc_final: 0.7440 (tmm-80) REVERT: K 21 MET cc_start: 0.8754 (mtm) cc_final: 0.8486 (mtm) REVERT: K 31 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8617 (mm) REVERT: K 50 ASN cc_start: 0.8948 (p0) cc_final: 0.8671 (p0) REVERT: L 128 MET cc_start: 0.8999 (tpt) cc_final: 0.8791 (tpt) REVERT: L 198 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8459 (mp) REVERT: L 202 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: L 401 THR cc_start: 0.9174 (m) cc_final: 0.8886 (p) REVERT: L 589 MET cc_start: 0.8209 (ttm) cc_final: 0.7585 (ttt) REVERT: M 200 MET cc_start: 0.8985 (mmt) cc_final: 0.8667 (mmm) REVERT: M 271 MET cc_start: 0.8362 (mmm) cc_final: 0.7968 (mtp) REVERT: M 308 SER cc_start: 0.9320 (m) cc_final: 0.8879 (p) REVERT: M 399 ASN cc_start: 0.8677 (t0) cc_final: 0.8401 (t0) REVERT: M 410 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8734 (ttp) REVERT: M 423 MET cc_start: 0.7283 (mmt) cc_final: 0.6123 (mmt) REVERT: N 43 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8496 (tpt) REVERT: N 126 MET cc_start: 0.7214 (mmt) cc_final: 0.6938 (mmp) REVERT: N 220 MET cc_start: 0.8335 (ptm) cc_final: 0.7973 (ptm) REVERT: N 246 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8468 (mp) REVERT: N 276 LEU cc_start: 0.8246 (pp) cc_final: 0.7904 (pp) REVERT: N 313 MET cc_start: 0.7579 (tpp) cc_final: 0.6866 (ttm) REVERT: N 317 GLN cc_start: 0.6818 (mp10) cc_final: 0.6547 (mp10) REVERT: O 55 GLU cc_start: 0.6277 (pp20) cc_final: 0.5883 (tm-30) REVERT: O 113 SER cc_start: 0.8288 (t) cc_final: 0.8005 (p) REVERT: O 116 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7368 (tttm) REVERT: O 120 ASP cc_start: 0.7369 (t0) cc_final: 0.7094 (t0) REVERT: O 182 GLN cc_start: 0.9089 (mp10) cc_final: 0.8878 (mp10) REVERT: O 185 ASP cc_start: 0.8834 (m-30) cc_final: 0.8534 (m-30) REVERT: O 202 HIS cc_start: 0.7494 (m170) cc_final: 0.7270 (m170) REVERT: O 235 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7567 (tp-100) REVERT: O 239 ASN cc_start: 0.7475 (m110) cc_final: 0.7060 (m110) REVERT: O 303 GLU cc_start: 0.7919 (tp30) cc_final: 0.7233 (tp30) REVERT: U 122 MET cc_start: 0.8586 (mmt) cc_final: 0.8265 (mmm) REVERT: U 156 GLU cc_start: 0.8018 (tp30) cc_final: 0.7794 (tp30) REVERT: Y 46 ASN cc_start: 0.8911 (t0) cc_final: 0.8555 (t0) REVERT: Y 85 LYS cc_start: 0.7297 (ptpt) cc_final: 0.7052 (ptpt) REVERT: c 47 SER cc_start: 0.8221 (m) cc_final: 0.7941 (p) REVERT: d 1 MET cc_start: 0.6561 (tpt) cc_final: 0.5573 (tpt) REVERT: d 34 MET cc_start: 0.8942 (mmm) cc_final: 0.8708 (mmm) REVERT: d 44 MET cc_start: 0.7056 (tpt) cc_final: 0.6589 (tpp) REVERT: e 5 ASP cc_start: 0.8544 (t0) cc_final: 0.8101 (t70) REVERT: e 82 GLN cc_start: 0.7858 (tp40) cc_final: 0.7165 (tt0) REVERT: e 83 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.6905 (mmt180) REVERT: e 87 MET cc_start: 0.8916 (ttm) cc_final: 0.8465 (mmt) REVERT: g 62 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: g 144 LYS cc_start: 0.9287 (mttm) cc_final: 0.8903 (mtpt) REVERT: h 72 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8222 (tttp) REVERT: h 90 ASN cc_start: 0.9075 (m-40) cc_final: 0.8537 (m-40) REVERT: i 13 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8255 (mt0) REVERT: i 27 GLU cc_start: 0.8803 (tt0) cc_final: 0.8422 (tt0) REVERT: i 87 LYS cc_start: 0.9409 (tttt) cc_final: 0.9112 (tttm) REVERT: i 101 LYS cc_start: 0.9087 (mttm) cc_final: 0.8718 (mttt) REVERT: i 112 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7914 (mt-10) REVERT: i 128 HIS cc_start: 0.6591 (t70) cc_final: 0.5538 (t-90) REVERT: j 88 ASP cc_start: 0.9119 (t0) cc_final: 0.8793 (t0) REVERT: j 91 GLN cc_start: 0.8937 (mt0) cc_final: 0.8577 (mm-40) REVERT: l 53 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8851 (tttm) REVERT: l 122 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8655 (p) REVERT: l 127 ASP cc_start: 0.8420 (m-30) cc_final: 0.8172 (m-30) REVERT: l 165 ASN cc_start: 0.9445 (t0) cc_final: 0.9147 (t0) REVERT: l 177 GLU cc_start: 0.8189 (mp0) cc_final: 0.7982 (mp0) REVERT: l 186 ILE cc_start: 0.7936 (mt) cc_final: 0.7414 (mm) REVERT: m 7 LYS cc_start: 0.8814 (tttm) cc_final: 0.8428 (ttpp) REVERT: m 62 ASP cc_start: 0.8811 (t0) cc_final: 0.8550 (t0) REVERT: m 95 PHE cc_start: 0.9079 (m-10) cc_final: 0.8579 (m-10) REVERT: p 15 SER cc_start: 0.8771 (m) cc_final: 0.7726 (p) REVERT: p 73 ASP cc_start: 0.8383 (p0) cc_final: 0.7882 (p0) REVERT: p 81 ASP cc_start: 0.8180 (t0) cc_final: 0.7961 (t0) REVERT: p 89 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: p 114 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8340 (tm-30) REVERT: p 137 LYS cc_start: 0.8613 (tppt) cc_final: 0.8254 (tptt) outliers start: 132 outliers final: 93 residues processed: 885 average time/residue: 0.1955 time to fit residues: 284.0429 Evaluate side-chains 883 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 781 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 202 MET Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 343 SER Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 112 CYS Chi-restraints excluded: chain O residue 127 ASN Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain X residue 171 THR Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 93 THR Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 95 GLU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain l residue 103 GLU Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 122 THR Chi-restraints excluded: chain l residue 149 VAL Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain l residue 175 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 80 CYS Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 89 GLU Chi-restraints excluded: chain p residue 125 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 171 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 183 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 292 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 HIS h 90 ASN ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 HIS j 54 GLN l 80 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102734 restraints weight = 48644.228| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.21 r_work: 0.3132 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32787 Z= 0.140 Angle : 0.657 14.849 44319 Z= 0.324 Chirality : 0.042 0.299 4815 Planarity : 0.005 0.064 5440 Dihedral : 12.001 170.506 5026 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.96 % Allowed : 20.01 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3782 helix: 1.14 (0.11), residues: 2448 sheet: -1.12 (1.46), residues: 18 loop : -0.42 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 295 TYR 0.027 0.001 TYR J 69 PHE 0.024 0.001 PHE M 122 TRP 0.017 0.001 TRP D 37 HIS 0.005 0.001 HIS j 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (32779) covalent geometry : angle 0.65584 / 0.32 (44303) SS BOND : bond 0.00458 / 0.24 ( 8) SS BOND : angle 2.21305 / 1.28 ( 16) hydrogen bonds : bond 0.04286 / 2.84 ( 1708) hydrogen bonds : angle 4.44224 / 3.23 ( 4950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 816 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 54 MET cc_start: 0.8600 (tmm) cc_final: 0.8219 (tmm) REVERT: J 144 MET cc_start: 0.8767 (mtp) cc_final: 0.8369 (mtm) REVERT: J 171 ARG cc_start: 0.7648 (tmm-80) cc_final: 0.7358 (tmm-80) REVERT: K 21 MET cc_start: 0.8652 (mtm) cc_final: 0.8355 (mtm) REVERT: K 31 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8584 (mm) REVERT: K 46 VAL cc_start: 0.8943 (t) cc_final: 0.8705 (t) REVERT: K 50 ASN cc_start: 0.8912 (p0) cc_final: 0.8653 (p0) REVERT: K 78 LEU cc_start: 0.8599 (tt) cc_final: 0.8384 (tp) REVERT: L 175 ASN cc_start: 0.8570 (m-40) cc_final: 0.8331 (m-40) REVERT: L 198 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8730 (mt) REVERT: L 202 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8341 (mtm) REVERT: L 401 THR cc_start: 0.9136 (m) cc_final: 0.8829 (p) REVERT: L 585 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8068 (mtpp) REVERT: L 589 MET cc_start: 0.8180 (ttm) cc_final: 0.7575 (ttt) REVERT: M 177 MET cc_start: 0.8294 (mmm) cc_final: 0.8090 (mmm) REVERT: M 200 MET cc_start: 0.8944 (mmt) cc_final: 0.8643 (mmm) REVERT: M 271 MET cc_start: 0.8286 (mmm) cc_final: 0.8023 (mtp) REVERT: M 393 ILE cc_start: 0.9137 (tp) cc_final: 0.8872 (tp) REVERT: M 399 ASN cc_start: 0.8616 (t0) cc_final: 0.8328 (t0) REVERT: M 423 MET cc_start: 0.7042 (mmt) cc_final: 0.6052 (mmt) REVERT: M 437 MET cc_start: 0.9234 (mpp) cc_final: 0.8798 (mmt) REVERT: M 447 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8770 (mp) REVERT: N 43 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8525 (tpt) REVERT: N 79 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8529 (tptp) REVERT: N 126 MET cc_start: 0.7188 (mmt) cc_final: 0.6697 (mmt) REVERT: N 220 MET cc_start: 0.8332 (ptm) cc_final: 0.7969 (ptm) REVERT: N 246 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8358 (mp) REVERT: N 271 MET cc_start: 0.9288 (mmm) cc_final: 0.9016 (mmm) REVERT: N 276 LEU cc_start: 0.8095 (pp) cc_final: 0.7643 (pp) REVERT: N 313 MET cc_start: 0.7683 (tpp) cc_final: 0.6967 (ttm) REVERT: N 317 GLN cc_start: 0.6735 (mp10) cc_final: 0.6035 (mp10) REVERT: O 55 GLU cc_start: 0.6220 (pp20) cc_final: 0.5851 (tm-30) REVERT: O 113 SER cc_start: 0.8426 (t) cc_final: 0.8092 (p) REVERT: O 116 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7464 (tttm) REVERT: O 120 ASP cc_start: 0.7719 (t0) cc_final: 0.7134 (t0) REVERT: O 185 ASP cc_start: 0.8809 (m-30) cc_final: 0.8507 (m-30) REVERT: O 202 HIS cc_start: 0.7655 (m170) cc_final: 0.7443 (m170) REVERT: O 235 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7752 (tm-30) REVERT: O 239 ASN cc_start: 0.7514 (m110) cc_final: 0.7084 (m110) REVERT: O 303 GLU cc_start: 0.7899 (tp30) cc_final: 0.7254 (tp30) REVERT: U 155 TYR cc_start: 0.9324 (p90) cc_final: 0.8767 (p90) REVERT: Y 46 ASN cc_start: 0.8944 (t0) cc_final: 0.8651 (t0) REVERT: Y 85 LYS cc_start: 0.7334 (ptpt) cc_final: 0.7100 (ptpt) REVERT: c 47 SER cc_start: 0.8235 (m) cc_final: 0.7968 (p) REVERT: d 1 MET cc_start: 0.6443 (tpt) cc_final: 0.5392 (tpt) REVERT: d 34 MET cc_start: 0.8944 (mmm) cc_final: 0.8718 (mmm) REVERT: d 44 MET cc_start: 0.7205 (tpt) cc_final: 0.6743 (tpp) REVERT: d 100 ASP cc_start: 0.8971 (m-30) cc_final: 0.8751 (m-30) REVERT: e 82 GLN cc_start: 0.7906 (tp40) cc_final: 0.7213 (tt0) REVERT: e 83 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6902 (mmt180) REVERT: e 86 LEU cc_start: 0.7587 (mp) cc_final: 0.7303 (mp) REVERT: e 87 MET cc_start: 0.8891 (ttm) cc_final: 0.8470 (mmt) REVERT: g 62 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: h 52 LYS cc_start: 0.8147 (tppt) cc_final: 0.7854 (tppt) REVERT: h 90 ASN cc_start: 0.8962 (m110) cc_final: 0.8593 (m110) REVERT: i 27 GLU cc_start: 0.8783 (tt0) cc_final: 0.8470 (tt0) REVERT: i 87 LYS cc_start: 0.9349 (tttt) cc_final: 0.9069 (tttm) REVERT: i 93 LYS cc_start: 0.8713 (mttm) cc_final: 0.8371 (mmtp) REVERT: i 101 LYS cc_start: 0.9014 (mttm) cc_final: 0.8623 (mttt) REVERT: i 112 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7850 (mt-10) REVERT: i 128 HIS cc_start: 0.6314 (t70) cc_final: 0.5164 (t-90) REVERT: j 43 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8434 (mmm-85) REVERT: j 88 ASP cc_start: 0.9096 (t0) cc_final: 0.8797 (t0) REVERT: l 53 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8798 (tttm) REVERT: l 165 ASN cc_start: 0.9441 (t0) cc_final: 0.9133 (t0) REVERT: l 186 ILE cc_start: 0.7855 (mt) cc_final: 0.7439 (mm) REVERT: m 5 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8892 (ttpt) REVERT: m 31 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8018 (ttt-90) REVERT: m 95 PHE cc_start: 0.9000 (m-10) cc_final: 0.8468 (m-10) REVERT: n 124 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8268 (mt0) REVERT: o 69 CYS cc_start: 0.6650 (OUTLIER) cc_final: 0.4096 (m) REVERT: p 15 SER cc_start: 0.8798 (m) cc_final: 0.7772 (p) REVERT: p 81 ASP cc_start: 0.7925 (t0) cc_final: 0.7651 (t0) REVERT: p 114 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8288 (tm-30) REVERT: p 137 LYS cc_start: 0.8586 (tppt) cc_final: 0.8273 (tptt) outliers start: 101 outliers final: 67 residues processed: 868 average time/residue: 0.1931 time to fit residues: 274.5740 Evaluate side-chains 856 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 780 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 202 MET Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 327 ILE Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 95 GLU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 141 GLN Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 69 CYS Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 285 optimal weight: 0.0770 chunk 253 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN M 304 GLN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 54 GLN l 80 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102269 restraints weight = 49081.967| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.25 r_work: 0.3127 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32787 Z= 0.148 Angle : 0.663 14.990 44319 Z= 0.327 Chirality : 0.043 0.292 4815 Planarity : 0.005 0.064 5440 Dihedral : 11.855 169.863 5026 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 2.87 % Allowed : 20.65 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3782 helix: 1.19 (0.11), residues: 2445 sheet: -1.03 (1.43), residues: 18 loop : -0.40 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 81 TYR 0.028 0.001 TYR J 69 PHE 0.024 0.001 PHE K 5 TRP 0.014 0.001 TRP N 114 HIS 0.004 0.001 HIS L 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (32779) covalent geometry : angle 0.66171 / 0.33 (44303) SS BOND : bond 0.00342 / 0.17 ( 8) SS BOND : angle 2.43448 / 1.46 ( 16) hydrogen bonds : bond 0.04269 / 2.81 ( 1708) hydrogen bonds : angle 4.41650 / 3.20 ( 4950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 805 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 54 MET cc_start: 0.8557 (tmm) cc_final: 0.8290 (tmm) REVERT: J 144 MET cc_start: 0.8749 (mtp) cc_final: 0.8345 (mtm) REVERT: J 171 ARG cc_start: 0.7589 (tmm-80) cc_final: 0.7245 (tmm-80) REVERT: K 21 MET cc_start: 0.8635 (mtm) cc_final: 0.8351 (mtm) REVERT: K 31 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (mm) REVERT: K 46 VAL cc_start: 0.8923 (t) cc_final: 0.8681 (t) REVERT: K 50 ASN cc_start: 0.8825 (p0) cc_final: 0.8600 (p0) REVERT: L 175 ASN cc_start: 0.8599 (m-40) cc_final: 0.8357 (m-40) REVERT: L 198 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8797 (mt) REVERT: L 202 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8397 (mtm) REVERT: L 317 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8778 (mt) REVERT: L 401 THR cc_start: 0.9128 (m) cc_final: 0.8797 (p) REVERT: L 451 MET cc_start: 0.8614 (mtm) cc_final: 0.8392 (mtm) REVERT: L 589 MET cc_start: 0.8174 (ttm) cc_final: 0.7551 (ttt) REVERT: M 200 MET cc_start: 0.8993 (mmt) cc_final: 0.8700 (mmm) REVERT: M 271 MET cc_start: 0.8255 (mmm) cc_final: 0.8013 (mtp) REVERT: M 393 ILE cc_start: 0.9133 (tp) cc_final: 0.8864 (tp) REVERT: M 399 ASN cc_start: 0.8667 (t0) cc_final: 0.8354 (t0) REVERT: M 423 MET cc_start: 0.7131 (mmt) cc_final: 0.6156 (mmt) REVERT: M 437 MET cc_start: 0.9229 (mpp) cc_final: 0.8795 (mmt) REVERT: M 447 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8817 (mp) REVERT: N 43 MET cc_start: 0.8865 (mmm) cc_final: 0.8466 (tpt) REVERT: N 79 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8607 (tptp) REVERT: N 126 MET cc_start: 0.7187 (mmt) cc_final: 0.6691 (mmt) REVERT: N 220 MET cc_start: 0.8224 (ptm) cc_final: 0.7848 (ptm) REVERT: N 246 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8185 (mp) REVERT: N 271 MET cc_start: 0.9291 (mmm) cc_final: 0.9008 (mmm) REVERT: N 276 LEU cc_start: 0.8037 (pp) cc_final: 0.7570 (pp) REVERT: N 313 MET cc_start: 0.7660 (tpp) cc_final: 0.6950 (ttm) REVERT: N 317 GLN cc_start: 0.6713 (mp10) cc_final: 0.6014 (mp10) REVERT: O 55 GLU cc_start: 0.6237 (pp20) cc_final: 0.5871 (tm-30) REVERT: O 113 SER cc_start: 0.8400 (t) cc_final: 0.8086 (p) REVERT: O 116 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7437 (tttm) REVERT: O 120 ASP cc_start: 0.7715 (t0) cc_final: 0.7124 (t0) REVERT: O 182 GLN cc_start: 0.9043 (mp10) cc_final: 0.8808 (mt0) REVERT: O 185 ASP cc_start: 0.8797 (m-30) cc_final: 0.8494 (m-30) REVERT: O 202 HIS cc_start: 0.7654 (m170) cc_final: 0.7431 (m170) REVERT: O 235 GLN cc_start: 0.8404 (tp-100) cc_final: 0.7769 (tm-30) REVERT: O 239 ASN cc_start: 0.7497 (m110) cc_final: 0.7069 (m110) REVERT: O 303 GLU cc_start: 0.7898 (tp30) cc_final: 0.7226 (tp30) REVERT: U 81 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: U 155 TYR cc_start: 0.9329 (p90) cc_final: 0.8817 (p90) REVERT: X 170 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.8173 (m-90) REVERT: Y 46 ASN cc_start: 0.8912 (t0) cc_final: 0.8643 (t0) REVERT: Y 85 LYS cc_start: 0.7391 (ptpt) cc_final: 0.7122 (ptpt) REVERT: c 47 SER cc_start: 0.8214 (m) cc_final: 0.7957 (p) REVERT: d 34 MET cc_start: 0.8943 (mmm) cc_final: 0.8727 (mmm) REVERT: d 44 MET cc_start: 0.7138 (tpt) cc_final: 0.6688 (tpp) REVERT: d 99 GLU cc_start: 0.9250 (pm20) cc_final: 0.8967 (pm20) REVERT: d 100 ASP cc_start: 0.8959 (m-30) cc_final: 0.8699 (m-30) REVERT: d 104 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7905 (mmmt) REVERT: e 82 GLN cc_start: 0.7878 (tp40) cc_final: 0.7184 (tt0) REVERT: e 83 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6888 (mmt180) REVERT: e 87 MET cc_start: 0.8900 (ttm) cc_final: 0.8470 (mmt) REVERT: g 62 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: h 52 LYS cc_start: 0.8168 (tppt) cc_final: 0.7825 (tppt) REVERT: h 90 ASN cc_start: 0.8967 (m110) cc_final: 0.8465 (m110) REVERT: i 27 GLU cc_start: 0.8791 (tt0) cc_final: 0.8434 (tt0) REVERT: i 87 LYS cc_start: 0.9352 (tttt) cc_final: 0.9103 (tttm) REVERT: i 93 LYS cc_start: 0.8709 (mttm) cc_final: 0.8438 (mmtp) REVERT: i 101 LYS cc_start: 0.9010 (mttm) cc_final: 0.8619 (mttt) REVERT: i 112 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8053 (mt-10) REVERT: i 128 HIS cc_start: 0.6318 (t70) cc_final: 0.5205 (t-90) REVERT: j 43 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: j 88 ASP cc_start: 0.9094 (t0) cc_final: 0.8786 (t0) REVERT: l 53 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8798 (tttm) REVERT: l 165 ASN cc_start: 0.9415 (t0) cc_final: 0.9124 (t0) REVERT: l 186 ILE cc_start: 0.7855 (mt) cc_final: 0.7450 (mm) REVERT: m 31 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8001 (ttt-90) REVERT: m 95 PHE cc_start: 0.8997 (m-10) cc_final: 0.8459 (m-10) REVERT: n 51 HIS cc_start: 0.7662 (m170) cc_final: 0.7447 (m170) REVERT: n 124 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8316 (mt0) REVERT: p 15 SER cc_start: 0.8842 (m) cc_final: 0.7807 (p) REVERT: p 81 ASP cc_start: 0.8106 (t0) cc_final: 0.7885 (t0) REVERT: p 114 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8314 (tm-30) REVERT: p 137 LYS cc_start: 0.8615 (tppt) cc_final: 0.8290 (tptt) outliers start: 98 outliers final: 75 residues processed: 854 average time/residue: 0.1924 time to fit residues: 268.5829 Evaluate side-chains 870 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 785 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 202 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 421 ASN Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 MET Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain X residue 170 TRP Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 109 SER Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain e residue 98 HIS Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 68 ASN Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 95 GLU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 141 GLN Chi-restraints excluded: chain o residue 28 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 4.9990 chunk 240 optimal weight: 0.0870 chunk 76 optimal weight: 0.0040 chunk 234 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 300 optimal weight: 0.0060 chunk 369 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 ASN c 73 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 80 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 54 GLN ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102451 restraints weight = 49014.062| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.23 r_work: 0.3127 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 32787 Z= 0.175 Angle : 0.844 59.199 44319 Z= 0.459 Chirality : 0.043 0.287 4815 Planarity : 0.005 0.064 5440 Dihedral : 11.858 169.877 5026 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 2.67 % Allowed : 21.06 % Favored : 76.27 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3782 helix: 1.20 (0.11), residues: 2445 sheet: -1.03 (1.43), residues: 18 loop : -0.40 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 147 TYR 0.026 0.001 TYR J 69 PHE 0.023 0.001 PHE M 122 TRP 0.020 0.001 TRP L 66 HIS 0.006 0.001 HIS M 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (32779) covalent geometry : angle 0.83551 / 0.46 (44303) SS BOND : bond 0.02890 / 2.21 ( 8) SS BOND : angle 6.30134 / 4.00 ( 16) hydrogen bonds : bond 0.04260 / 2.81 ( 1708) hydrogen bonds : angle 4.41757 / 3.21 ( 4950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7564 Ramachandran restraints generated. 3782 Oldfield, 0 Emsley, 3782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 788 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 54 MET cc_start: 0.8530 (tmm) cc_final: 0.8278 (tmm) REVERT: J 144 MET cc_start: 0.8751 (mtp) cc_final: 0.8352 (mtm) REVERT: J 171 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.7255 (tmm-80) REVERT: K 21 MET cc_start: 0.8644 (mtm) cc_final: 0.8362 (mtm) REVERT: K 31 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8577 (mm) REVERT: K 46 VAL cc_start: 0.8934 (t) cc_final: 0.8686 (t) REVERT: K 50 ASN cc_start: 0.8822 (p0) cc_final: 0.8595 (p0) REVERT: L 175 ASN cc_start: 0.8598 (m-40) cc_final: 0.8354 (m-40) REVERT: L 198 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8806 (mt) REVERT: L 202 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8397 (mtm) REVERT: L 317 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (mt) REVERT: L 401 THR cc_start: 0.9129 (m) cc_final: 0.8799 (p) REVERT: L 451 MET cc_start: 0.8628 (mtm) cc_final: 0.8406 (mtm) REVERT: L 585 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8016 (mtpp) REVERT: L 589 MET cc_start: 0.8182 (ttm) cc_final: 0.7576 (ttt) REVERT: M 200 MET cc_start: 0.8999 (mmt) cc_final: 0.8713 (mmm) REVERT: M 271 MET cc_start: 0.8254 (mmm) cc_final: 0.8011 (mtp) REVERT: M 393 ILE cc_start: 0.9132 (tp) cc_final: 0.8866 (tp) REVERT: M 399 ASN cc_start: 0.8664 (t0) cc_final: 0.8357 (t0) REVERT: M 423 MET cc_start: 0.7147 (mmt) cc_final: 0.6123 (mmt) REVERT: M 437 MET cc_start: 0.9224 (mpp) cc_final: 0.8791 (mmt) REVERT: M 447 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8821 (mp) REVERT: N 43 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8468 (tpt) REVERT: N 79 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8616 (tptp) REVERT: N 126 MET cc_start: 0.7201 (mmt) cc_final: 0.6712 (mmt) REVERT: N 220 MET cc_start: 0.8233 (ptm) cc_final: 0.7856 (ptm) REVERT: N 246 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8192 (mp) REVERT: N 271 MET cc_start: 0.9295 (mmm) cc_final: 0.9006 (mmm) REVERT: N 276 LEU cc_start: 0.8043 (pp) cc_final: 0.7582 (pp) REVERT: N 313 MET cc_start: 0.7664 (tpp) cc_final: 0.6960 (ttm) REVERT: N 317 GLN cc_start: 0.6719 (mp10) cc_final: 0.6018 (mp10) REVERT: O 55 GLU cc_start: 0.6245 (pp20) cc_final: 0.5874 (tm-30) REVERT: O 113 SER cc_start: 0.8357 (t) cc_final: 0.8085 (p) REVERT: O 116 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7440 (tttm) REVERT: O 120 ASP cc_start: 0.7727 (t0) cc_final: 0.7138 (t0) REVERT: O 182 GLN cc_start: 0.9101 (mp10) cc_final: 0.8816 (mt0) REVERT: O 185 ASP cc_start: 0.8803 (m-30) cc_final: 0.8499 (m-30) REVERT: O 202 HIS cc_start: 0.7660 (m170) cc_final: 0.7441 (m170) REVERT: O 235 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7764 (tm-30) REVERT: O 239 ASN cc_start: 0.7492 (m110) cc_final: 0.7073 (m110) REVERT: O 289 TRP cc_start: 0.7446 (m100) cc_final: 0.7210 (m100) REVERT: O 303 GLU cc_start: 0.7898 (tp30) cc_final: 0.7227 (tp30) REVERT: U 81 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: U 155 TYR cc_start: 0.9321 (p90) cc_final: 0.8812 (p90) REVERT: X 170 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.8182 (m-90) REVERT: Y 46 ASN cc_start: 0.8910 (t0) cc_final: 0.8644 (t0) REVERT: Y 85 LYS cc_start: 0.7380 (ptpt) cc_final: 0.7104 (ptpt) REVERT: c 47 SER cc_start: 0.8222 (m) cc_final: 0.7963 (p) REVERT: d 34 MET cc_start: 0.8950 (mmm) cc_final: 0.8737 (mmm) REVERT: d 44 MET cc_start: 0.7137 (tpt) cc_final: 0.6686 (tpp) REVERT: d 99 GLU cc_start: 0.9242 (pm20) cc_final: 0.8960 (pm20) REVERT: d 100 ASP cc_start: 0.8941 (m-30) cc_final: 0.8689 (m-30) REVERT: e 82 GLN cc_start: 0.7885 (tp40) cc_final: 0.7185 (tt0) REVERT: e 83 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6896 (mmt180) REVERT: e 87 MET cc_start: 0.8901 (ttm) cc_final: 0.8473 (mmt) REVERT: f 12 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8906 (t) REVERT: g 62 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: h 52 LYS cc_start: 0.8162 (tppt) cc_final: 0.7830 (tppt) REVERT: h 90 ASN cc_start: 0.8971 (m110) cc_final: 0.8466 (m110) REVERT: i 27 GLU cc_start: 0.8793 (tt0) cc_final: 0.8438 (tt0) REVERT: i 87 LYS cc_start: 0.9363 (tttt) cc_final: 0.9111 (tttm) REVERT: i 93 LYS cc_start: 0.8713 (mttm) cc_final: 0.8435 (mmtp) REVERT: i 101 LYS cc_start: 0.9017 (mttm) cc_final: 0.8633 (mttt) REVERT: i 112 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8057 (mt-10) REVERT: i 128 HIS cc_start: 0.6327 (t70) cc_final: 0.5204 (t-90) REVERT: j 43 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: j 88 ASP cc_start: 0.9110 (t0) cc_final: 0.8806 (t0) REVERT: l 53 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8794 (tttm) REVERT: l 165 ASN cc_start: 0.9418 (t0) cc_final: 0.9128 (t0) REVERT: l 186 ILE cc_start: 0.7855 (mt) cc_final: 0.7458 (mm) REVERT: m 31 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8010 (ttt-90) REVERT: m 95 PHE cc_start: 0.9009 (m-10) cc_final: 0.8474 (m-10) REVERT: n 51 HIS cc_start: 0.7666 (m170) cc_final: 0.7452 (m170) REVERT: n 124 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8320 (mt0) REVERT: p 15 SER cc_start: 0.8852 (m) cc_final: 0.7828 (p) REVERT: p 81 ASP cc_start: 0.8142 (t0) cc_final: 0.7892 (t0) REVERT: p 114 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8315 (tm-30) REVERT: p 137 LYS cc_start: 0.8612 (tppt) cc_final: 0.8302 (tptt) outliers start: 91 outliers final: 74 residues processed: 833 average time/residue: 0.1896 time to fit residues: 258.3581 Evaluate side-chains 867 residues out of total 3409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 781 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 202 MET Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 359 MET Chi-restraints excluded: chain L residue 433 THR Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 83 HIS Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 421 ASN Chi-restraints excluded: chain M residue 447 LEU Chi-restraints excluded: chain M residue 457 LEU Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 187 MET Chi-restraints excluded: chain N residue 206 MET Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 285 MET Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 127 ASN Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 290 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain X residue 170 TRP Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 50 MET Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain e residue 93 THR Chi-restraints excluded: chain f residue 11 TRP Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain g residue 62 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 60 SER Chi-restraints excluded: chain h residue 95 GLU Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 104 ILE Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain i residue 127 HIS Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain l residue 168 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 127 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 85 SER Chi-restraints excluded: chain n residue 141 GLN Chi-restraints excluded: chain o residue 28 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain p residue 9 VAL Chi-restraints excluded: chain p residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 179 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 332 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 ASN c 73 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 54 GLN l 80 ASN l 100 ASN ** m 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102447 restraints weight = 48662.198| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.3128 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 32787 Z= 0.199 Angle : 0.933 59.165 44319 Z= 0.540 Chirality : 0.059 2.141 4815 Planarity : 0.005 0.089 5440 Dihedral : 11.860 169.879 5026 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 2.67 % Allowed : 21.03 % Favored : 76.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3782 helix: 1.20 (0.11), residues: 2445 sheet: -1.03 (1.43), residues: 18 loop : -0.42 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 147 TYR 0.025 0.001 TYR J 69 PHE 0.024 0.001 PHE M 122 TRP 0.020 0.001 TRP L 66 HIS 0.007 0.001 HIS M 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (32779) covalent geometry : angle 0.92713 / 0.54 (44303) SS BOND : bond 0.01109 / 0.87 ( 8) SS BOND : angle 5.75206 / 3.63 ( 16) hydrogen bonds : bond 0.04262 / 2.81 ( 1708) hydrogen bonds : angle 4.41949 / 3.21 ( 4950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9921.62 seconds wall clock time: 170 minutes 34.83 seconds (10234.83 seconds total)