Starting phenix.real_space_refine on Fri Feb 16 21:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4x_21050/02_2024/6v4x_21050.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 52 5.49 5 S 101 5.16 5 C 10276 2.51 5 N 2881 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I ARG 29": "NH1" <-> "NH2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 180": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "I ARG 211": "NH1" <-> "NH2" Residue "I ARG 212": "NH1" <-> "NH2" Residue "I ARG 215": "NH1" <-> "NH2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I ARG 242": "NH1" <-> "NH2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 306": "NH1" <-> "NH2" Residue "I ARG 319": "NH1" <-> "NH2" Residue "I ARG 339": "NH1" <-> "NH2" Residue "I ARG 366": "NH1" <-> "NH2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ARG 534": "NH1" <-> "NH2" Residue "I ARG 543": "NH1" <-> "NH2" Residue "I ARG 559": "NH1" <-> "NH2" Residue "I GLU 602": "OE1" <-> "OE2" Residue "J ARG 218": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16499 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "E" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 670 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 911 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "D" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "H" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3980 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Chain: "I" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4055 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 22, 'TRANS': 487} Chain breaks: 2 Chain: "J" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2461 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "Z" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 564 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 20} Chain: "Y" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 537 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.65, per 1000 atoms: 0.58 Number of scatterers: 16499 At special positions: 0 Unit cell: (117.7, 149.8, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 52 15.00 O 3187 8.00 N 2881 7.00 C 10276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 71 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 158 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 73 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 418 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 76 " 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 22 sheets defined 34.4% alpha, 23.5% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.713A pdb=" N ASN A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.669A pdb=" N HIS B 12 " --> pdb=" O MET B 9 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.530A pdb=" N LEU E 20 " --> pdb=" O GLN E 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.907A pdb=" N ILE C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.976A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 106 removed outlier: 3.589A pdb=" N GLU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.714A pdb=" N GLU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.600A pdb=" N LEU H 53 " --> pdb=" O MET H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.542A pdb=" N GLU H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 60 through 64' Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 96 through 107 removed outlier: 3.708A pdb=" N ALA H 101 " --> pdb=" O HIS H 97 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TRP H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.816A pdb=" N GLU H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 232 removed outlier: 3.578A pdb=" N ALA H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 3.532A pdb=" N LEU H 251 " --> pdb=" O GLN H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 265 removed outlier: 3.561A pdb=" N LEU H 263 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS H 264 " --> pdb=" O PRO H 261 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP H 265 " --> pdb=" O GLU H 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 260 through 265' Processing helix chain 'H' and resid 273 through 278 removed outlier: 3.668A pdb=" N LYS H 277 " --> pdb=" O SER H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 285 removed outlier: 3.731A pdb=" N TYR H 282 " --> pdb=" O CYS H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 335 through 343 removed outlier: 3.777A pdb=" N PHE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 368 through 370 No H-bonds generated for 'chain 'H' and resid 368 through 370' Processing helix chain 'H' and resid 398 through 410 removed outlier: 3.840A pdb=" N GLU H 404 " --> pdb=" O GLN H 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 409 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 433 removed outlier: 3.543A pdb=" N LEU H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 472 removed outlier: 3.863A pdb=" N ASP H 472 " --> pdb=" O PHE H 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 88 through 107 removed outlier: 3.722A pdb=" N MET I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 103 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 211 through 229 removed outlier: 3.704A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN I 218 " --> pdb=" O GLN I 214 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 226 " --> pdb=" O ASN I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 256 removed outlier: 3.504A pdb=" N ILE I 253 " --> pdb=" O LEU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 264 removed outlier: 3.917A pdb=" N VAL I 263 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 281 removed outlier: 3.506A pdb=" N VAL I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 297 removed outlier: 4.144A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 318 Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 363 through 370 Processing helix chain 'I' and resid 548 through 556 removed outlier: 4.116A pdb=" N ILE I 553 " --> pdb=" O ILE I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 579 removed outlier: 3.594A pdb=" N GLN I 572 " --> pdb=" O PRO I 568 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP I 573 " --> pdb=" O GLU I 569 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS I 577 " --> pdb=" O ASP I 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 44 removed outlier: 4.489A pdb=" N VAL J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP J 38 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 4.364A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 70 Processing helix chain 'J' and resid 73 through 78 removed outlier: 3.521A pdb=" N ILE J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.759A pdb=" N ALA J 82 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP J 83 " --> pdb=" O PHE J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'J' and resid 85 through 101 removed outlier: 4.113A pdb=" N ARG J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE J 93 " --> pdb=" O ARG J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 106 through 111 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 147 removed outlier: 3.816A pdb=" N VAL J 126 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER J 147 " --> pdb=" O TRP J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 removed outlier: 3.584A pdb=" N CYS J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE J 168 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 192 removed outlier: 3.827A pdb=" N GLY J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 244 removed outlier: 3.874A pdb=" N LYS J 233 " --> pdb=" O TRP J 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 244 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 266 removed outlier: 3.688A pdb=" N GLY J 258 " --> pdb=" O THR J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 269 No H-bonds generated for 'chain 'J' and resid 267 through 269' Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.667A pdb=" N ILE J 275 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 310 removed outlier: 4.369A pdb=" N SER J 296 " --> pdb=" O SER J 292 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 310 " --> pdb=" O LEU J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 316 removed outlier: 3.806A pdb=" N LEU J 315 " --> pdb=" O PRO J 312 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 328 removed outlier: 3.534A pdb=" N THR J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL J 326 " --> pdb=" O THR J 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP J 327 " --> pdb=" O THR J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 337 removed outlier: 3.601A pdb=" N ILE J 335 " --> pdb=" O PRO J 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.795A pdb=" N ALA A 56 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 48 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 28 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 16 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 17 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 73 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 19 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 71 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 21 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 28 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.212A pdb=" N SER A 44 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 32 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY A 30 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 48 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 28 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 16 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 17 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 73 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 19 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 71 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 21 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG B 16 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 53 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.522A pdb=" N ILE F 72 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN F 43 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 64 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA F 45 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 62 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU F 49 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS F 58 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE F 51 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER F 56 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU D 358 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LYS D 168 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.522A pdb=" N ILE F 72 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS F 22 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE F 72 " --> pdb=" O MET F 20 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 20 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR F 32 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN F 46 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 34 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 44 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 36 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET F 42 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN F 43 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 64 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA F 45 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 62 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU F 49 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS F 58 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE F 51 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER F 56 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU D 358 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LYS D 168 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL D 171 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL D 182 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 173 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG D 180 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR D 205 " --> pdb=" O PHE D 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 75 removed outlier: 6.083A pdb=" N ALA E 61 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 56 removed outlier: 6.498A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS G 45 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN G 28 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU G 47 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N HIS G 26 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 71 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET G 69 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.637A pdb=" N THR C 30 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.674A pdb=" N TYR C 59 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.251A pdb=" N THR H 93 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU H 67 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 66 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYS H 27 " --> pdb=" O LEU H 17 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 144 through 145 removed outlier: 6.802A pdb=" N LYS H 173 " --> pdb=" O ILE H 200 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE H 202 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU H 175 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLU H 204 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU H 201 " --> pdb=" O ILE H 415 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL H 417 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE H 203 " --> pdb=" O VAL H 417 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL H 414 " --> pdb=" O HIS H 446 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.646A pdb=" N ILE H 268 " --> pdb=" O SER H 309 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG H 235 " --> pdb=" O GLY H 351 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE H 353 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU H 237 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 373 through 375 Processing sheet with id=AB5, first strand: chain 'H' and resid 462 through 466 removed outlier: 4.376A pdb=" N LYS H 462 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 466 " --> pdb=" O TYR I 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 606 " --> pdb=" O VAL H 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 492 through 495 Processing sheet with id=AB7, first strand: chain 'I' and resid 29 through 30 removed outlier: 6.644A pdb=" N CYS I 20 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.649A pdb=" N VAL I 58 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR I 87 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE I 84 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU I 129 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA I 86 " --> pdb=" O LEU I 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AC1, first strand: chain 'I' and resid 149 through 150 Processing sheet with id=AC2, first strand: chain 'I' and resid 172 through 173 removed outlier: 6.175A pdb=" N LEU I 198 " --> pdb=" O ILE I 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 308 through 311 removed outlier: 6.329A pdb=" N LEU I 266 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS I 311 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU I 268 " --> pdb=" O CYS I 311 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU I 327 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL I 233 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA I 328 " --> pdb=" O VAL I 233 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE I 235 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU I 234 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE I 353 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 377 through 384 547 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3900 1.33 - 1.45: 3441 1.45 - 1.57: 9290 1.57 - 1.69: 101 1.69 - 1.81: 170 Bond restraints: 16902 Sorted by residual: bond pdb=" O3' G Y 46 " pdb=" P U Y 47 " ideal model delta sigma weight residual 1.607 1.695 -0.088 1.50e-02 4.44e+03 3.41e+01 bond pdb=" O3' A Y 48 " pdb=" P A Y 49 " ideal model delta sigma weight residual 1.607 1.688 -0.081 1.50e-02 4.44e+03 2.92e+01 bond pdb=" CA PRO H 267 " pdb=" C PRO H 267 " ideal model delta sigma weight residual 1.520 1.562 -0.043 1.42e-02 4.96e+03 9.13e+00 bond pdb=" O3' U Y 47 " pdb=" P A Y 48 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.53e+00 bond pdb=" C PRO F 7 " pdb=" N LYS F 8 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.07e-02 2.33e+03 5.77e+00 ... (remaining 16897 not shown) Histogram of bond angle deviations from ideal: 81.30 - 92.89: 1 92.89 - 104.47: 449 104.47 - 116.06: 11295 116.06 - 127.65: 11089 127.65 - 139.23: 236 Bond angle restraints: 23070 Sorted by residual: angle pdb=" C3' A Y 48 " pdb=" O3' A Y 48 " pdb=" P A Y 49 " ideal model delta sigma weight residual 120.20 139.23 -19.03 1.50e+00 4.44e-01 1.61e+02 angle pdb=" N ALA H 507 " pdb=" CA ALA H 507 " pdb=" C ALA H 507 " ideal model delta sigma weight residual 111.14 123.25 -12.11 1.08e+00 8.57e-01 1.26e+02 angle pdb=" O3' A Y 48 " pdb=" P A Y 49 " pdb=" OP1 A Y 49 " ideal model delta sigma weight residual 108.00 81.30 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C3' U Y 47 " pdb=" O3' U Y 47 " pdb=" P A Y 48 " ideal model delta sigma weight residual 120.20 107.88 12.32 1.50e+00 4.44e-01 6.75e+01 angle pdb=" O3' A Y 48 " pdb=" P A Y 49 " pdb=" OP2 A Y 49 " ideal model delta sigma weight residual 108.00 131.83 -23.83 3.00e+00 1.11e-01 6.31e+01 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 10073 32.54 - 65.08: 241 65.08 - 97.62: 20 97.62 - 130.16: 2 130.16 - 162.70: 1 Dihedral angle restraints: 10337 sinusoidal: 4736 harmonic: 5601 Sorted by residual: dihedral pdb=" C5' G Z 26 " pdb=" C4' G Z 26 " pdb=" C3' G Z 26 " pdb=" O3' G Z 26 " ideal model delta sinusoidal sigma weight residual 147.00 85.93 61.07 1 8.00e+00 1.56e-02 7.74e+01 dihedral pdb=" O4' G Z 26 " pdb=" C4' G Z 26 " pdb=" C3' G Z 26 " pdb=" C2' G Z 26 " ideal model delta sinusoidal sigma weight residual 24.00 -30.20 54.20 1 8.00e+00 1.56e-02 6.22e+01 dihedral pdb=" C4' G Z 26 " pdb=" C3' G Z 26 " pdb=" C2' G Z 26 " pdb=" C1' G Z 26 " ideal model delta sinusoidal sigma weight residual -35.00 11.13 -46.13 1 8.00e+00 1.56e-02 4.61e+01 ... (remaining 10334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2245 0.079 - 0.158: 396 0.158 - 0.237: 29 0.237 - 0.316: 8 0.316 - 0.395: 3 Chirality restraints: 2681 Sorted by residual: chirality pdb=" CA ALA H 507 " pdb=" N ALA H 507 " pdb=" C ALA H 507 " pdb=" CB ALA H 507 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB VAL I 272 " pdb=" CA VAL I 272 " pdb=" CG1 VAL I 272 " pdb=" CG2 VAL I 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CB ILE H 494 " pdb=" CA ILE H 494 " pdb=" CG1 ILE H 494 " pdb=" CG2 ILE H 494 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2678 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 600 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C THR I 600 " 0.062 2.00e-02 2.50e+03 pdb=" O THR I 600 " -0.023 2.00e-02 2.50e+03 pdb=" N SER I 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 194 " -0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO I 195 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 345 " 0.029 2.00e-02 2.50e+03 1.99e-02 9.93e+00 pdb=" CG TRP I 345 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP I 345 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP I 345 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 345 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 345 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 345 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 345 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 345 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 345 " 0.003 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 196 2.61 - 3.19: 13216 3.19 - 3.76: 25754 3.76 - 4.33: 36804 4.33 - 4.90: 60178 Nonbonded interactions: 136148 Sorted by model distance: nonbonded pdb=" OD2 ASP H 179 " pdb="ZN ZN H 702 " model vdw 2.043 2.230 nonbonded pdb=" O2' G Z 26 " pdb=" OP2 U Z 27 " model vdw 2.183 2.440 nonbonded pdb=" O LEU H 500 " pdb=" O THR H 504 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP H 75 " pdb="ZN ZN H 702 " model vdw 2.261 2.230 nonbonded pdb=" OG1 THR A 24 " pdb=" OE1 GLU A 26 " model vdw 2.293 2.440 ... (remaining 136143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.010 Extract box with map and model: 8.880 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 53.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 16902 Z= 0.420 Angle : 1.012 26.702 23070 Z= 0.549 Chirality : 0.060 0.395 2681 Planarity : 0.007 0.086 2755 Dihedral : 13.607 162.702 6703 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 0.93 % Allowed : 5.14 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.15), residues: 1899 helix: -4.40 (0.09), residues: 602 sheet: -2.62 (0.23), residues: 402 loop : -2.30 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP I 345 HIS 0.013 0.002 HIS I 183 PHE 0.035 0.003 PHE I 620 TYR 0.041 0.003 TYR E 24 ARG 0.011 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 395 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8197 (tt0) cc_final: 0.7944 (tt0) REVERT: E 18 ILE cc_start: 0.8707 (tp) cc_final: 0.8418 (tp) REVERT: C 6 SER cc_start: 0.8592 (t) cc_final: 0.8344 (p) REVERT: D 142 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7334 (mtp85) REVERT: H 58 LEU cc_start: 0.8799 (mm) cc_final: 0.8572 (mp) REVERT: H 312 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7157 (tttm) REVERT: H 313 SER cc_start: 0.8647 (t) cc_final: 0.8234 (p) REVERT: I 92 LYS cc_start: 0.8122 (mttm) cc_final: 0.7883 (mtpp) REVERT: I 98 MET cc_start: 0.9023 (mmm) cc_final: 0.8626 (mmm) REVERT: J 144 MET cc_start: 0.8680 (mmm) cc_final: 0.8246 (mmm) outliers start: 16 outliers final: 7 residues processed: 408 average time/residue: 0.3384 time to fit residues: 198.7317 Evaluate side-chains 279 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 699 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.0670 chunk 146 optimal weight: 0.0030 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN E 19 ASN E 83 ASN G 39 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN D 160 HIS D 352 ASN H 97 HIS ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN H 301 ASN H 307 HIS H 502 ASN I 39 HIS I 62 HIS I 204 ASN I 607 GLN I 619 GLN J 41 ASN J 64 ASN J 304 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16902 Z= 0.185 Angle : 0.630 11.257 23070 Z= 0.323 Chirality : 0.045 0.210 2681 Planarity : 0.005 0.050 2755 Dihedral : 14.376 105.875 2868 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.57 % Allowed : 8.82 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.17), residues: 1899 helix: -2.45 (0.17), residues: 605 sheet: -2.13 (0.24), residues: 399 loop : -1.90 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 345 HIS 0.009 0.001 HIS I 565 PHE 0.017 0.001 PHE J 91 TYR 0.015 0.001 TYR I 21 ARG 0.005 0.000 ARG I 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 306 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 78 LYS cc_start: 0.7832 (ptpp) cc_final: 0.7397 (ptpt) REVERT: E 28 ARG cc_start: 0.7575 (tpt90) cc_final: 0.7312 (tpt-90) REVERT: D 142 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7297 (mtp85) REVERT: D 177 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8225 (mttm) REVERT: H 312 LYS cc_start: 0.7447 (ttmt) cc_final: 0.7005 (tttp) REVERT: H 363 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8905 (tm) REVERT: H 370 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H 467 MET cc_start: 0.5575 (pmt) cc_final: 0.5320 (pmt) REVERT: I 98 MET cc_start: 0.9137 (mmm) cc_final: 0.8595 (mmm) REVERT: J 205 ARG cc_start: 0.6273 (pmt170) cc_final: 0.5398 (ptt90) REVERT: J 307 SER cc_start: 0.7136 (t) cc_final: 0.6449 (m) outliers start: 44 outliers final: 19 residues processed: 336 average time/residue: 0.3373 time to fit residues: 161.3814 Evaluate side-chains 278 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 0.0040 chunk 48 optimal weight: 0.4980 chunk 175 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 0.0970 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN C 22 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS H 227 HIS H 231 ASN H 316 HIS I 51 HIS I 218 GLN I 248 GLN J 293 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16902 Z= 0.155 Angle : 0.552 8.866 23070 Z= 0.283 Chirality : 0.043 0.360 2681 Planarity : 0.004 0.043 2755 Dihedral : 13.836 106.411 2856 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.28 % Allowed : 10.98 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 1899 helix: -1.15 (0.20), residues: 601 sheet: -1.73 (0.25), residues: 390 loop : -1.55 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 345 HIS 0.008 0.001 HIS I 565 PHE 0.012 0.001 PHE I 620 TYR 0.014 0.001 TYR I 606 ARG 0.005 0.000 ARG J 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 28 ARG cc_start: 0.7497 (tpt90) cc_final: 0.7272 (tpt-90) REVERT: C 89 ASN cc_start: 0.8010 (t0) cc_final: 0.7514 (t0) REVERT: D 142 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7333 (mtp85) REVERT: D 177 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8275 (mttt) REVERT: H 106 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8779 (tp) REVERT: H 312 LYS cc_start: 0.7579 (ttmt) cc_final: 0.7163 (tttp) REVERT: H 370 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7428 (mm-30) REVERT: I 19 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7926 (mm) REVERT: I 98 MET cc_start: 0.9061 (mmm) cc_final: 0.8768 (mmm) REVERT: J 205 ARG cc_start: 0.6412 (pmt170) cc_final: 0.5501 (ptt90) REVERT: J 307 SER cc_start: 0.6957 (t) cc_final: 0.6297 (m) outliers start: 39 outliers final: 25 residues processed: 301 average time/residue: 0.3144 time to fit residues: 137.5600 Evaluate side-chains 281 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 170 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN C 78 ASN D 342 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS H 258 GLN I 218 GLN ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16902 Z= 0.469 Angle : 0.709 11.424 23070 Z= 0.359 Chirality : 0.049 0.213 2681 Planarity : 0.004 0.045 2755 Dihedral : 14.181 117.097 2856 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.80 % Allowed : 11.04 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.18), residues: 1899 helix: -0.95 (0.20), residues: 607 sheet: -1.93 (0.25), residues: 393 loop : -1.41 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP I 345 HIS 0.009 0.002 HIS B 12 PHE 0.022 0.002 PHE I 620 TYR 0.020 0.002 TYR E 24 ARG 0.008 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 273 time to evaluate : 2.065 Fit side-chains REVERT: E 62 GLU cc_start: 0.8424 (pt0) cc_final: 0.8162 (pt0) REVERT: C 15 ASN cc_start: 0.9048 (m-40) cc_final: 0.8787 (m110) REVERT: C 45 ASN cc_start: 0.7342 (t0) cc_final: 0.7127 (t0) REVERT: C 89 ASN cc_start: 0.8183 (t0) cc_final: 0.7924 (t0) REVERT: D 142 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7296 (mtp85) REVERT: D 177 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8409 (mtpp) REVERT: H 312 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7512 (tttp) REVERT: H 370 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7575 (mm-30) REVERT: I 98 MET cc_start: 0.9037 (mmm) cc_final: 0.8736 (mmm) REVERT: I 592 LYS cc_start: 0.8301 (mtmp) cc_final: 0.8033 (mtmm) REVERT: J 144 MET cc_start: 0.8962 (tpp) cc_final: 0.8721 (mmm) outliers start: 65 outliers final: 49 residues processed: 319 average time/residue: 0.3369 time to fit residues: 159.9465 Evaluate side-chains 305 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 415 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16902 Z= 0.319 Angle : 0.620 9.316 23070 Z= 0.314 Chirality : 0.046 0.244 2681 Planarity : 0.004 0.045 2755 Dihedral : 14.007 111.617 2856 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.32 % Allowed : 11.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1899 helix: -0.57 (0.21), residues: 602 sheet: -1.74 (0.25), residues: 381 loop : -1.29 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 345 HIS 0.008 0.001 HIS B 12 PHE 0.018 0.002 PHE I 620 TYR 0.015 0.002 TYR I 606 ARG 0.006 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7626 (ptpt) REVERT: E 62 GLU cc_start: 0.8394 (pt0) cc_final: 0.8165 (pt0) REVERT: C 15 ASN cc_start: 0.9055 (m-40) cc_final: 0.8829 (m-40) REVERT: C 89 ASN cc_start: 0.8132 (t0) cc_final: 0.7705 (t0) REVERT: D 142 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7508 (mtp85) REVERT: D 148 MET cc_start: 0.8476 (mmm) cc_final: 0.8250 (mtp) REVERT: D 177 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8427 (mtpp) REVERT: H 312 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7394 (tttm) REVERT: H 370 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7568 (mm-30) REVERT: I 592 LYS cc_start: 0.8275 (mtmp) cc_final: 0.7978 (mtmm) REVERT: J 84 LYS cc_start: 0.8480 (tmmt) cc_final: 0.8102 (ttpp) REVERT: J 144 MET cc_start: 0.8868 (tpp) cc_final: 0.8559 (mmm) outliers start: 74 outliers final: 53 residues processed: 317 average time/residue: 0.2916 time to fit residues: 137.5636 Evaluate side-chains 312 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 259 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 300 ASN J 81 GLN J 207 GLN ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16902 Z= 0.192 Angle : 0.565 9.126 23070 Z= 0.282 Chirality : 0.043 0.218 2681 Planarity : 0.003 0.038 2755 Dihedral : 13.790 108.222 2856 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.62 % Allowed : 13.38 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1899 helix: -0.18 (0.22), residues: 603 sheet: -1.57 (0.26), residues: 373 loop : -1.12 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 345 HIS 0.007 0.001 HIS I 565 PHE 0.011 0.001 PHE B 31 TYR 0.012 0.001 TYR I 21 ARG 0.005 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 275 time to evaluate : 2.024 Fit side-chains REVERT: A 78 LYS cc_start: 0.7813 (ptpp) cc_final: 0.7603 (ptpt) REVERT: E 62 GLU cc_start: 0.8360 (pt0) cc_final: 0.8083 (pt0) REVERT: D 142 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7164 (mtp85) REVERT: D 177 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8262 (mtpp) REVERT: H 312 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7206 (tttm) REVERT: H 370 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7494 (mm-30) REVERT: I 180 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7872 (ptm-80) REVERT: I 592 LYS cc_start: 0.8208 (mtmp) cc_final: 0.7840 (mmtt) REVERT: J 84 LYS cc_start: 0.8427 (tmmt) cc_final: 0.8075 (ttpp) REVERT: J 133 MET cc_start: 0.8706 (mmm) cc_final: 0.8088 (mmm) REVERT: J 144 MET cc_start: 0.8797 (tpp) cc_final: 0.8505 (tpp) REVERT: J 167 ASP cc_start: 0.7942 (t0) cc_final: 0.7686 (m-30) REVERT: J 307 SER cc_start: 0.6985 (t) cc_final: 0.6333 (m) outliers start: 62 outliers final: 47 residues processed: 312 average time/residue: 0.3053 time to fit residues: 139.8519 Evaluate side-chains 309 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 262 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 315 SER Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN C 15 ASN H 11 GLN H 231 ASN I 54 GLN I 607 GLN ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16902 Z= 0.274 Angle : 0.596 10.916 23070 Z= 0.299 Chirality : 0.045 0.223 2681 Planarity : 0.003 0.040 2755 Dihedral : 13.803 110.665 2856 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.15 % Allowed : 13.32 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1899 helix: -0.08 (0.22), residues: 604 sheet: -1.45 (0.25), residues: 391 loop : -1.06 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 345 HIS 0.006 0.001 HIS B 12 PHE 0.017 0.001 PHE I 620 TYR 0.012 0.001 TYR E 24 ARG 0.008 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 263 time to evaluate : 1.841 Fit side-chains REVERT: A 44 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 78 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7670 (ptpt) REVERT: E 62 GLU cc_start: 0.8461 (pt0) cc_final: 0.8189 (pt0) REVERT: D 142 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7200 (mtp85) REVERT: D 148 MET cc_start: 0.8460 (mmm) cc_final: 0.8224 (mtp) REVERT: D 177 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8304 (mtpp) REVERT: H 132 MET cc_start: 0.9004 (mmm) cc_final: 0.8671 (mmm) REVERT: H 312 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7351 (tttm) REVERT: H 370 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7584 (mm-30) REVERT: H 374 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9266 (pp) REVERT: I 96 MET cc_start: 0.8851 (tpp) cc_final: 0.8522 (mmt) REVERT: I 180 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7937 (ptm-80) REVERT: I 592 LYS cc_start: 0.8215 (mtmp) cc_final: 0.7922 (mtmm) REVERT: J 84 LYS cc_start: 0.8502 (tmmt) cc_final: 0.8115 (ttpp) REVERT: J 133 MET cc_start: 0.8762 (mmm) cc_final: 0.8183 (mmm) REVERT: J 144 MET cc_start: 0.8824 (tpp) cc_final: 0.8081 (mmt) REVERT: J 167 ASP cc_start: 0.7969 (t0) cc_final: 0.7714 (m-30) outliers start: 71 outliers final: 59 residues processed: 311 average time/residue: 0.2954 time to fit residues: 137.2636 Evaluate side-chains 317 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 256 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 315 SER Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN J 81 GLN ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16902 Z= 0.255 Angle : 0.589 10.711 23070 Z= 0.295 Chirality : 0.044 0.219 2681 Planarity : 0.003 0.041 2755 Dihedral : 13.745 109.488 2856 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.03 % Allowed : 13.43 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1899 helix: -0.06 (0.22), residues: 611 sheet: -1.46 (0.26), residues: 379 loop : -0.99 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 345 HIS 0.006 0.001 HIS I 565 PHE 0.015 0.001 PHE I 620 TYR 0.011 0.001 TYR I 21 ARG 0.006 0.000 ARG H 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 2.018 Fit side-chains REVERT: A 76 MET cc_start: 0.8403 (ppp) cc_final: 0.8035 (ppp) REVERT: A 77 LEU cc_start: 0.8677 (tp) cc_final: 0.7996 (mp) REVERT: A 78 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7666 (ptpt) REVERT: B 65 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7826 (mtm110) REVERT: E 62 GLU cc_start: 0.8465 (pt0) cc_final: 0.8212 (pt0) REVERT: C 107 PHE cc_start: 0.7348 (t80) cc_final: 0.7115 (t80) REVERT: D 142 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7209 (mtp85) REVERT: D 177 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8286 (mtpp) REVERT: H 312 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7336 (tttm) REVERT: H 370 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7589 (mm-30) REVERT: I 96 MET cc_start: 0.8840 (tpp) cc_final: 0.8513 (mmt) REVERT: I 180 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7935 (ptm-80) REVERT: I 592 LYS cc_start: 0.8196 (mtmp) cc_final: 0.7905 (mtmm) REVERT: J 84 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8178 (ttpp) REVERT: J 133 MET cc_start: 0.8730 (mmm) cc_final: 0.8148 (mmm) REVERT: J 144 MET cc_start: 0.8807 (tpp) cc_final: 0.8048 (mmt) REVERT: J 167 ASP cc_start: 0.7981 (t0) cc_final: 0.7725 (m-30) REVERT: J 307 SER cc_start: 0.7125 (t) cc_final: 0.6409 (m) outliers start: 69 outliers final: 58 residues processed: 307 average time/residue: 0.3029 time to fit residues: 138.0608 Evaluate side-chains 314 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 315 SER Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.4980 chunk 162 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16902 Z= 0.215 Angle : 0.575 9.897 23070 Z= 0.286 Chirality : 0.044 0.223 2681 Planarity : 0.003 0.041 2755 Dihedral : 13.662 107.721 2856 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.74 % Allowed : 13.90 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1899 helix: 0.09 (0.22), residues: 609 sheet: -1.42 (0.26), residues: 379 loop : -0.93 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 345 HIS 0.006 0.001 HIS I 565 PHE 0.013 0.001 PHE I 620 TYR 0.010 0.001 TYR H 103 ARG 0.006 0.000 ARG H 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 264 time to evaluate : 1.755 Fit side-chains REVERT: A 76 MET cc_start: 0.8455 (ppp) cc_final: 0.8035 (ppp) REVERT: A 77 LEU cc_start: 0.8694 (tp) cc_final: 0.8035 (mp) REVERT: A 78 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7672 (ptpt) REVERT: B 65 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7809 (mtm110) REVERT: E 62 GLU cc_start: 0.8447 (pt0) cc_final: 0.8185 (pt0) REVERT: G 26 HIS cc_start: 0.7811 (t-170) cc_final: 0.7546 (t-170) REVERT: C 107 PHE cc_start: 0.7291 (t80) cc_final: 0.7036 (t80) REVERT: D 142 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7244 (mtp85) REVERT: D 177 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8245 (mtpp) REVERT: H 312 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7266 (tttm) REVERT: H 370 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7585 (mm-30) REVERT: I 96 MET cc_start: 0.8790 (tpp) cc_final: 0.8460 (mmt) REVERT: I 180 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7928 (ptm-80) REVERT: I 265 SER cc_start: 0.8941 (m) cc_final: 0.8362 (t) REVERT: I 592 LYS cc_start: 0.8184 (mtmp) cc_final: 0.7890 (mtmm) REVERT: J 84 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8147 (ttpp) REVERT: J 133 MET cc_start: 0.8696 (mmm) cc_final: 0.8118 (mmm) REVERT: J 144 MET cc_start: 0.8783 (tpp) cc_final: 0.8013 (mmt) REVERT: J 167 ASP cc_start: 0.7977 (t0) cc_final: 0.7725 (m-30) REVERT: J 307 SER cc_start: 0.7110 (t) cc_final: 0.6390 (m) outliers start: 64 outliers final: 54 residues processed: 305 average time/residue: 0.3004 time to fit residues: 136.3437 Evaluate side-chains 309 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 255 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 315 SER Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN G 39 ASN D 160 HIS ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16902 Z= 0.302 Angle : 0.617 10.718 23070 Z= 0.306 Chirality : 0.045 0.215 2681 Planarity : 0.003 0.041 2755 Dihedral : 13.732 110.541 2856 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.74 % Allowed : 14.31 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1899 helix: 0.04 (0.22), residues: 609 sheet: -1.45 (0.26), residues: 379 loop : -0.92 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 345 HIS 0.006 0.001 HIS B 12 PHE 0.016 0.001 PHE I 620 TYR 0.011 0.002 TYR E 24 ARG 0.006 0.000 ARG H 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 253 time to evaluate : 2.018 Fit side-chains REVERT: A 76 MET cc_start: 0.8486 (ppp) cc_final: 0.8047 (ppp) REVERT: A 77 LEU cc_start: 0.8708 (tp) cc_final: 0.8051 (mp) REVERT: A 78 LYS cc_start: 0.8067 (ptpp) cc_final: 0.7696 (ptpt) REVERT: B 65 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7814 (mtm110) REVERT: E 62 GLU cc_start: 0.8455 (pt0) cc_final: 0.8214 (pt0) REVERT: G 26 HIS cc_start: 0.7868 (t-170) cc_final: 0.7587 (t-170) REVERT: C 107 PHE cc_start: 0.7456 (t80) cc_final: 0.7186 (t80) REVERT: D 142 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7259 (mtp85) REVERT: D 177 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8274 (mtpp) REVERT: H 312 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7364 (tttm) REVERT: H 370 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7581 (mm-30) REVERT: H 374 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9256 (pp) REVERT: H 462 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7927 (ptmt) REVERT: I 96 MET cc_start: 0.8842 (tpp) cc_final: 0.8512 (mmt) REVERT: I 180 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7922 (ptm-80) REVERT: I 592 LYS cc_start: 0.8173 (mtmp) cc_final: 0.7876 (mtmm) REVERT: J 133 MET cc_start: 0.8736 (mmm) cc_final: 0.8175 (mmm) REVERT: J 144 MET cc_start: 0.8811 (tpp) cc_final: 0.8022 (mmt) REVERT: J 167 ASP cc_start: 0.7997 (t0) cc_final: 0.7743 (m-30) outliers start: 64 outliers final: 58 residues processed: 295 average time/residue: 0.2968 time to fit residues: 129.8225 Evaluate side-chains 310 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 250 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain F residue 25 TRP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 41 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 357 TYR Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 439 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 462 LYS Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 315 SER Chi-restraints excluded: chain I residue 376 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 562 ILE Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 565 HIS Chi-restraints excluded: chain I residue 588 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 281 LEU Chi-restraints excluded: chain J residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114922 restraints weight = 20463.077| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.59 r_work: 0.3246 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16902 Z= 0.221 Angle : 0.579 10.273 23070 Z= 0.287 Chirality : 0.044 0.219 2681 Planarity : 0.003 0.041 2755 Dihedral : 13.628 107.715 2856 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.56 % Allowed : 14.60 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1899 helix: 0.18 (0.22), residues: 609 sheet: -1.40 (0.26), residues: 379 loop : -0.86 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 345 HIS 0.006 0.001 HIS I 565 PHE 0.013 0.001 PHE I 620 TYR 0.010 0.001 TYR H 103 ARG 0.006 0.000 ARG H 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.58 seconds wall clock time: 73 minutes 20.89 seconds (4400.89 seconds total)