Starting phenix.real_space_refine on Wed Feb 14 07:28:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r81_4749/02_2024/6r81_4749_neut_updated.pdb" } resolution = 3.9 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= 0.010 sd= 0.063 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 P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 544": "OD1" <-> "OD2" Residue "B GLU 575": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8861 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4405 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4392 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.59 Number of scatterers: 8861 At special positions: 0 Unit cell: (75.26, 90.1, 137.8, 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) S 35 16.00 P 6 15.00 Mg 2 11.99 O 1671 8.00 N 1479 7.00 C 5668 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 4 sheets defined 57.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.598A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 59 removed outlier: 3.680A pdb=" N TYR A 26 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU A 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 30 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 35 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 43 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 4.385A pdb=" N THR A 50 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 51 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 54 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 55 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 108 removed outlier: 4.036A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 125 through 158 removed outlier: 4.450A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.746A pdb=" N ALA A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 4.187A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.992A pdb=" N ARG A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.658A pdb=" N TYR A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 268 removed outlier: 3.753A pdb=" N ARG A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 245 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 250 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.851A pdb=" N LEU A 256 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N MET A 259 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 263 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 268 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 321 removed outlier: 3.527A pdb=" N VAL A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.856A pdb=" N GLN A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N MET A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 321 " --> pdb=" O MET A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.550A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.721A pdb=" N ALA A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.519A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 524 removed outlier: 4.033A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.720A pdb=" N ALA A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.634A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.749A pdb=" N GLU A 585 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 586 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.600A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 57 removed outlier: 3.681A pdb=" N TYR B 26 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 30 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 42 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 43 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 4.394A pdb=" N THR B 50 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS B 51 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 54 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 108 removed outlier: 4.217A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 125 through 158 removed outlier: 4.450A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 173 through 195 removed outlier: 3.758A pdb=" N ALA B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.198A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 210 through 216 removed outlier: 4.993A pdb=" N ARG B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.658A pdb=" N TYR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 268 removed outlier: 3.753A pdb=" N ARG B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 245 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 250 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.848A pdb=" N LEU B 256 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N MET B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR B 268 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 321 removed outlier: 3.535A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix removed outlier: 3.861A pdb=" N GLN B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 321 " --> pdb=" O MET B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.898A pdb=" N LEU B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.723A pdb=" N ALA B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 495 removed outlier: 3.520A pdb=" N ARG B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 removed outlier: 4.034A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.723A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.634A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing sheet with id= A, first strand: chain 'A' and resid 397 through 400 removed outlier: 4.819A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.742A pdb=" N GLN A 545 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR A 530 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 372 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 532 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLY A 374 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.818A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.745A pdb=" N GLN B 545 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR B 530 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 372 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 532 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLY B 374 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1451 1.26 - 1.40: 2010 1.40 - 1.54: 5398 1.54 - 1.68: 68 1.68 - 1.82: 68 Bond restraints: 8995 Sorted by residual: bond pdb=" CA SER A 480 " pdb=" C SER A 480 " ideal model delta sigma weight residual 1.532 1.410 0.121 1.15e-02 7.56e+03 1.11e+02 bond pdb=" C THR B 381 " pdb=" O THR B 381 " ideal model delta sigma weight residual 1.237 1.125 0.111 1.19e-02 7.06e+03 8.73e+01 bond pdb=" C LYS B 380 " pdb=" O LYS B 380 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.26e-02 6.30e+03 8.35e+01 bond pdb=" CA THR B 382 " pdb=" C THR B 382 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.34e-02 5.57e+03 6.60e+01 bond pdb=" C ILE A 477 " pdb=" O ILE A 477 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.23e-02 6.61e+03 6.45e+01 ... (remaining 8990 not shown) Histogram of bond angle deviations from ideal: 89.20 - 98.72: 4 98.72 - 108.24: 462 108.24 - 117.75: 6334 117.75 - 127.27: 5298 127.27 - 136.78: 86 Bond angle restraints: 12184 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" C SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta sigma weight residual 114.40 89.20 25.20 1.25e+00 6.40e-01 4.06e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.39 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.58 17.29 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.05 15.78 1.00e+00 1.00e+00 2.49e+02 ... (remaining 12179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4731 17.89 - 35.78: 582 35.78 - 53.66: 122 53.66 - 71.55: 27 71.55 - 89.44: 16 Dihedral angle restraints: 5478 sinusoidal: 2207 harmonic: 3271 Sorted by residual: dihedral pdb=" C SER A 480 " pdb=" N SER A 480 " pdb=" CA SER A 480 " pdb=" CB SER A 480 " ideal model delta harmonic sigma weight residual -122.60 -92.81 -29.79 0 2.50e+00 1.60e-01 1.42e+02 dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 132.04 47.96 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 132.39 47.61 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 5475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1411 0.147 - 0.294: 51 0.294 - 0.440: 6 0.440 - 0.587: 0 0.587 - 0.734: 1 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CA ARG A 475 " pdb=" N ARG A 475 " pdb=" C ARG A 475 " pdb=" CB ARG A 475 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA MET B 59 " pdb=" N MET B 59 " pdb=" C MET B 59 " pdb=" CB MET B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA SER B 60 " pdb=" N SER B 60 " pdb=" C SER B 60 " pdb=" CB SER B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1466 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 58 " 0.045 2.00e-02 2.50e+03 9.41e-02 8.85e+01 pdb=" C SER B 58 " -0.162 2.00e-02 2.50e+03 pdb=" O SER B 58 " 0.064 2.00e-02 2.50e+03 pdb=" N MET B 59 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 480 " -0.027 2.00e-02 2.50e+03 5.23e-02 2.73e+01 pdb=" C SER A 480 " 0.090 2.00e-02 2.50e+03 pdb=" O SER A 480 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY A 481 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 474 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLU A 474 " 0.089 2.00e-02 2.50e+03 pdb=" O GLU A 474 " -0.033 2.00e-02 2.50e+03 pdb=" N ARG A 475 " -0.030 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 20 2.21 - 2.88: 3647 2.88 - 3.56: 13241 3.56 - 4.23: 20039 4.23 - 4.90: 32124 Nonbonded interactions: 69071 Sorted by model distance: nonbonded pdb=" O GLY B 374 " pdb=" NZ LYS B 380 " model vdw 1.538 2.520 nonbonded pdb=" OG SER A 480 " pdb=" N GLY A 481 " model vdw 1.887 2.520 nonbonded pdb=" O ARG B 432 " pdb=" SG CYS B 436 " model vdw 1.912 3.400 nonbonded pdb=" N GLY B 374 " pdb=" CE LYS B 380 " model vdw 1.919 3.520 nonbonded pdb=" O ARG A 432 " pdb=" SG CYS A 436 " model vdw 1.933 3.400 ... (remaining 69066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 269 or resid 282 through 586 or resid 603)) selection = (chain 'B' and (resid 9 through 269 or resid 282 through 586 or resid 601)) } 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 group one per residue 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: 0.430 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: 2.160 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.050 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.011 0.154 8995 Z= 0.715 Angle : 1.495 25.197 12184 Z= 0.951 Chirality : 0.073 0.734 1469 Planarity : 0.009 0.094 1518 Dihedral : 16.775 89.439 3374 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.47 % Favored : 88.08 % Rotamer: Outliers : 1.25 % Allowed : 14.35 % Favored : 84.41 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.09 % 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: -5.27 (0.18), residues: 1133 helix: -3.59 (0.12), residues: 597 sheet: -2.99 (0.64), residues: 50 loop : -3.28 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 413 HIS 0.012 0.003 HIS B 141 PHE 0.027 0.004 PHE A 57 TYR 0.023 0.003 TYR B 570 ARG 0.014 0.002 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4646 (t0) REVERT: A 101 GLU cc_start: 0.9225 (tp30) cc_final: 0.8826 (tp30) REVERT: A 158 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8898 (tp) REVERT: A 231 MET cc_start: 0.9205 (ttm) cc_final: 0.8862 (tpp) REVERT: A 262 LEU cc_start: 0.9228 (mm) cc_final: 0.8995 (mm) REVERT: A 295 MET cc_start: 0.9061 (tpp) cc_final: 0.8647 (tmm) REVERT: A 299 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9005 (mm-40) REVERT: A 474 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 478 MET cc_start: 0.8990 (mmm) cc_final: 0.8457 (mmm) REVERT: B 145 PHE cc_start: 0.9396 (t80) cc_final: 0.8624 (t80) REVERT: B 158 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 231 MET cc_start: 0.9226 (ttm) cc_final: 0.8879 (tpp) REVERT: B 288 LEU cc_start: 0.8945 (tt) cc_final: 0.8741 (tt) REVERT: B 295 MET cc_start: 0.9109 (tpp) cc_final: 0.8486 (tmm) REVERT: B 299 GLN cc_start: 0.9470 (mm-40) cc_final: 0.8910 (mm-40) REVERT: B 413 TRP cc_start: 0.8688 (t60) cc_final: 0.7630 (t60) outliers start: 12 outliers final: 3 residues processed: 221 average time/residue: 0.1814 time to fit residues: 57.1485 Evaluate side-chains 179 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 459 ASN A 518 GLN B 196 GLN B 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8995 Z= 0.223 Angle : 0.761 9.088 12184 Z= 0.394 Chirality : 0.044 0.239 1469 Planarity : 0.005 0.057 1518 Dihedral : 9.836 75.413 1301 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.09 % Favored : 90.56 % Rotamer: Outliers : 4.37 % Allowed : 20.37 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.60 (0.22), residues: 1133 helix: -2.11 (0.17), residues: 620 sheet: -2.24 (0.68), residues: 50 loop : -2.64 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 413 HIS 0.009 0.002 HIS A 567 PHE 0.021 0.002 PHE A 74 TYR 0.022 0.002 TYR B 350 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.9031 (tp30) cc_final: 0.8586 (tp30) REVERT: A 145 PHE cc_start: 0.9185 (t80) cc_final: 0.8694 (t80) REVERT: A 231 MET cc_start: 0.8903 (ttm) cc_final: 0.8535 (tpp) REVERT: A 262 LEU cc_start: 0.9459 (mm) cc_final: 0.9169 (mm) REVERT: A 289 TYR cc_start: 0.7760 (m-10) cc_final: 0.7532 (m-80) REVERT: A 299 GLN cc_start: 0.9487 (mm-40) cc_final: 0.9078 (mm110) REVERT: A 460 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 567 HIS cc_start: 0.7574 (t70) cc_final: 0.7277 (t-90) REVERT: B 145 PHE cc_start: 0.9283 (t80) cc_final: 0.8743 (t80) REVERT: B 231 MET cc_start: 0.9021 (ttm) cc_final: 0.8658 (tpp) REVERT: B 262 LEU cc_start: 0.9488 (mm) cc_final: 0.9150 (mm) REVERT: B 295 MET cc_start: 0.9189 (tpp) cc_final: 0.8710 (tmm) REVERT: B 299 GLN cc_start: 0.9455 (mm-40) cc_final: 0.8984 (mm110) REVERT: B 413 TRP cc_start: 0.8698 (t60) cc_final: 0.7792 (t60) REVERT: B 433 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8707 (mt-10) REVERT: B 460 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7449 (t80) outliers start: 42 outliers final: 22 residues processed: 227 average time/residue: 0.1735 time to fit residues: 56.9391 Evaluate side-chains 200 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 207 ASN B 66 GLN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8995 Z= 0.260 Angle : 0.734 7.751 12184 Z= 0.375 Chirality : 0.043 0.194 1469 Planarity : 0.004 0.051 1518 Dihedral : 9.105 72.996 1287 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.12 % Favored : 88.70 % Rotamer: Outliers : 5.93 % Allowed : 22.97 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.68 (0.24), residues: 1133 helix: -1.25 (0.20), residues: 615 sheet: -2.02 (0.64), residues: 60 loop : -2.37 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 413 HIS 0.007 0.002 HIS A 141 PHE 0.015 0.001 PHE B 348 TYR 0.014 0.002 TYR B 570 ARG 0.005 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9130 (t80) cc_final: 0.8710 (t80) REVERT: A 162 MET cc_start: 0.8282 (tpp) cc_final: 0.7927 (tmm) REVERT: A 231 MET cc_start: 0.8912 (ttm) cc_final: 0.8501 (tpp) REVERT: A 262 LEU cc_start: 0.9499 (mm) cc_final: 0.9202 (mm) REVERT: A 288 LEU cc_start: 0.8970 (tt) cc_final: 0.8695 (pp) REVERT: A 289 TYR cc_start: 0.7864 (m-10) cc_final: 0.7636 (m-80) REVERT: A 295 MET cc_start: 0.9101 (tmm) cc_final: 0.8893 (tmm) REVERT: A 299 GLN cc_start: 0.9500 (mm-40) cc_final: 0.9065 (mm110) REVERT: A 460 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7346 (t80) REVERT: A 466 ASN cc_start: 0.7940 (t0) cc_final: 0.7650 (t0) REVERT: B 122 GLU cc_start: 0.8608 (tt0) cc_final: 0.8273 (tt0) REVERT: B 145 PHE cc_start: 0.9264 (t80) cc_final: 0.8682 (t80) REVERT: B 162 MET cc_start: 0.8133 (tpp) cc_final: 0.7647 (tmm) REVERT: B 188 MET cc_start: 0.8821 (tpp) cc_final: 0.8600 (mmm) REVERT: B 231 MET cc_start: 0.9054 (ttm) cc_final: 0.8643 (tpp) REVERT: B 262 LEU cc_start: 0.9517 (mm) cc_final: 0.9283 (mm) REVERT: B 299 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9097 (mm110) outliers start: 57 outliers final: 38 residues processed: 220 average time/residue: 0.1649 time to fit residues: 53.6980 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8995 Z= 0.196 Angle : 0.689 8.584 12184 Z= 0.347 Chirality : 0.041 0.132 1469 Planarity : 0.004 0.051 1518 Dihedral : 8.797 71.355 1287 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 5.09 % Allowed : 25.99 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.29 (0.25), residues: 1133 helix: -0.87 (0.21), residues: 618 sheet: -1.67 (0.66), residues: 60 loop : -2.33 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.006 0.001 HIS A 141 PHE 0.013 0.001 PHE B 348 TYR 0.012 0.001 TYR B 570 ARG 0.004 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9315 (ppp) cc_final: 0.9020 (ppp) REVERT: A 145 PHE cc_start: 0.9121 (t80) cc_final: 0.8746 (t80) REVERT: A 162 MET cc_start: 0.8228 (tpp) cc_final: 0.7860 (tmm) REVERT: A 231 MET cc_start: 0.8955 (ttm) cc_final: 0.8368 (tpp) REVERT: A 262 LEU cc_start: 0.9509 (mm) cc_final: 0.9254 (mm) REVERT: A 288 LEU cc_start: 0.8992 (tt) cc_final: 0.8737 (pp) REVERT: A 289 TYR cc_start: 0.7822 (m-10) cc_final: 0.7555 (m-80) REVERT: A 295 MET cc_start: 0.9106 (tmm) cc_final: 0.8898 (tmm) REVERT: A 299 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9058 (mm110) REVERT: A 460 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 466 ASN cc_start: 0.7967 (t0) cc_final: 0.7673 (t0) REVERT: B 145 PHE cc_start: 0.9256 (t80) cc_final: 0.8660 (t80) REVERT: B 219 SER cc_start: 0.8202 (t) cc_final: 0.7714 (p) REVERT: B 231 MET cc_start: 0.8987 (ttm) cc_final: 0.8480 (tpp) REVERT: B 262 LEU cc_start: 0.9516 (mm) cc_final: 0.9246 (mm) REVERT: B 299 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9012 (mm110) REVERT: B 314 THR cc_start: 0.9257 (p) cc_final: 0.8975 (t) outliers start: 49 outliers final: 35 residues processed: 218 average time/residue: 0.1649 time to fit residues: 52.9288 Evaluate side-chains 217 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8995 Z= 0.167 Angle : 0.669 7.346 12184 Z= 0.333 Chirality : 0.041 0.143 1469 Planarity : 0.004 0.049 1518 Dihedral : 8.461 76.178 1287 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 5.51 % Allowed : 26.40 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -2.02 (0.25), residues: 1133 helix: -0.66 (0.21), residues: 619 sheet: -1.34 (0.68), residues: 60 loop : -2.23 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS B 141 PHE 0.010 0.001 PHE B 115 TYR 0.013 0.001 TYR B 570 ARG 0.007 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9039 (t80) cc_final: 0.8702 (t80) REVERT: A 191 ILE cc_start: 0.9481 (mm) cc_final: 0.8987 (tt) REVERT: A 262 LEU cc_start: 0.9545 (mm) cc_final: 0.9278 (mm) REVERT: A 289 TYR cc_start: 0.7747 (m-10) cc_final: 0.7476 (m-80) REVERT: A 295 MET cc_start: 0.9057 (tmm) cc_final: 0.8834 (tmm) REVERT: A 299 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9059 (mm110) REVERT: A 433 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8853 (mt-10) REVERT: A 460 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7374 (t80) REVERT: A 466 ASN cc_start: 0.7927 (t0) cc_final: 0.7668 (t0) REVERT: B 145 PHE cc_start: 0.9224 (t80) cc_final: 0.8632 (t80) REVERT: B 219 SER cc_start: 0.8120 (t) cc_final: 0.7610 (p) REVERT: B 231 MET cc_start: 0.9010 (ttm) cc_final: 0.8413 (tpp) REVERT: B 243 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8985 (tm-30) REVERT: B 262 LEU cc_start: 0.9511 (mm) cc_final: 0.9228 (mm) REVERT: B 288 LEU cc_start: 0.8853 (tt) cc_final: 0.8598 (pp) REVERT: B 295 MET cc_start: 0.9083 (tmm) cc_final: 0.8565 (tmm) REVERT: B 299 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9050 (mm-40) REVERT: B 314 THR cc_start: 0.9210 (p) cc_final: 0.8883 (t) REVERT: B 318 ILE cc_start: 0.9355 (mm) cc_final: 0.9072 (mm) REVERT: B 433 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8710 (mt-10) outliers start: 53 outliers final: 36 residues processed: 229 average time/residue: 0.1978 time to fit residues: 65.4259 Evaluate side-chains 233 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8995 Z= 0.208 Angle : 0.686 12.351 12184 Z= 0.340 Chirality : 0.042 0.128 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.379 76.061 1287 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 5.61 % Allowed : 29.00 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.84 (0.26), residues: 1133 helix: -0.57 (0.21), residues: 633 sheet: -1.31 (0.65), residues: 60 loop : -2.08 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 413 HIS 0.005 0.001 HIS B 141 PHE 0.010 0.001 PHE A 348 TYR 0.017 0.001 TYR B 350 ARG 0.007 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9107 (t80) cc_final: 0.8760 (t80) REVERT: A 210 LEU cc_start: 0.9589 (tp) cc_final: 0.9232 (tp) REVERT: A 262 LEU cc_start: 0.9555 (mm) cc_final: 0.9300 (mm) REVERT: A 299 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9081 (mm110) REVERT: A 466 ASN cc_start: 0.7928 (t0) cc_final: 0.7696 (t0) REVERT: B 145 PHE cc_start: 0.9233 (t80) cc_final: 0.8635 (t80) REVERT: B 191 ILE cc_start: 0.9496 (tp) cc_final: 0.9044 (tt) REVERT: B 219 SER cc_start: 0.8138 (t) cc_final: 0.7608 (p) REVERT: B 243 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8888 (tm-30) REVERT: B 262 LEU cc_start: 0.9540 (mm) cc_final: 0.9263 (mm) REVERT: B 288 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 295 MET cc_start: 0.9104 (tmm) cc_final: 0.8584 (tmm) REVERT: B 299 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9066 (mm-40) REVERT: B 314 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8861 (t) REVERT: B 318 ILE cc_start: 0.9365 (mm) cc_final: 0.9104 (mm) REVERT: B 326 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8417 (tm-30) outliers start: 54 outliers final: 37 residues processed: 227 average time/residue: 0.1554 time to fit residues: 52.3400 Evaluate side-chains 228 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8995 Z= 0.172 Angle : 0.703 11.186 12184 Z= 0.341 Chirality : 0.041 0.131 1469 Planarity : 0.004 0.046 1518 Dihedral : 8.240 77.012 1287 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 5.82 % Allowed : 29.73 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1133 helix: -0.54 (0.21), residues: 642 sheet: -0.97 (0.66), residues: 55 loop : -2.17 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 104 HIS 0.004 0.001 HIS B 141 PHE 0.013 0.001 PHE B 115 TYR 0.014 0.001 TYR A 408 ARG 0.005 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9072 (t80) cc_final: 0.8747 (t80) REVERT: A 191 ILE cc_start: 0.9475 (tp) cc_final: 0.9097 (tt) REVERT: A 210 LEU cc_start: 0.9560 (tp) cc_final: 0.9244 (tp) REVERT: A 262 LEU cc_start: 0.9536 (mm) cc_final: 0.9266 (mm) REVERT: A 295 MET cc_start: 0.9021 (tmm) cc_final: 0.8747 (tmm) REVERT: A 299 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8937 (mm-40) REVERT: A 388 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8723 (mm-30) REVERT: A 501 MET cc_start: 0.9104 (tpp) cc_final: 0.8596 (tpp) REVERT: B 122 GLU cc_start: 0.8577 (tt0) cc_final: 0.8336 (tt0) REVERT: B 145 PHE cc_start: 0.9158 (t80) cc_final: 0.8577 (t80) REVERT: B 191 ILE cc_start: 0.9477 (tp) cc_final: 0.9107 (tt) REVERT: B 219 SER cc_start: 0.8186 (t) cc_final: 0.7680 (p) REVERT: B 243 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8841 (tm-30) REVERT: B 262 LEU cc_start: 0.9497 (mm) cc_final: 0.9220 (mm) REVERT: B 288 LEU cc_start: 0.8963 (tt) cc_final: 0.8751 (pp) REVERT: B 295 MET cc_start: 0.9133 (tmm) cc_final: 0.8613 (tmm) REVERT: B 299 GLN cc_start: 0.9458 (mm-40) cc_final: 0.9069 (mm-40) REVERT: B 326 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8307 (pp20) outliers start: 56 outliers final: 40 residues processed: 230 average time/residue: 0.1693 time to fit residues: 56.8481 Evaluate side-chains 229 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8995 Z= 0.161 Angle : 0.720 10.457 12184 Z= 0.343 Chirality : 0.042 0.198 1469 Planarity : 0.004 0.059 1518 Dihedral : 8.089 78.703 1287 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.47 % Allowed : 31.60 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.66 (0.25), residues: 1133 helix: -0.38 (0.21), residues: 620 sheet: -0.58 (0.70), residues: 50 loop : -2.13 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 104 HIS 0.003 0.001 HIS B 141 PHE 0.008 0.001 PHE A 348 TYR 0.015 0.001 TYR B 408 ARG 0.010 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9056 (t80) cc_final: 0.8740 (t80) REVERT: A 191 ILE cc_start: 0.9501 (tp) cc_final: 0.9142 (tt) REVERT: A 262 LEU cc_start: 0.9547 (mm) cc_final: 0.9283 (mm) REVERT: A 295 MET cc_start: 0.8966 (tmm) cc_final: 0.8630 (tmm) REVERT: A 299 GLN cc_start: 0.9462 (mm-40) cc_final: 0.9051 (mm-40) REVERT: A 326 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (tm-30) REVERT: A 388 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8625 (mm-30) REVERT: A 501 MET cc_start: 0.9119 (tpp) cc_final: 0.8735 (tpp) REVERT: B 122 GLU cc_start: 0.8649 (tt0) cc_final: 0.8405 (tt0) REVERT: B 145 PHE cc_start: 0.9158 (t80) cc_final: 0.8583 (t80) REVERT: B 184 ILE cc_start: 0.9594 (mm) cc_final: 0.9370 (tp) REVERT: B 191 ILE cc_start: 0.9508 (tp) cc_final: 0.9160 (tt) REVERT: B 219 SER cc_start: 0.8143 (t) cc_final: 0.7636 (p) REVERT: B 243 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8859 (tm-30) REVERT: B 262 LEU cc_start: 0.9485 (mm) cc_final: 0.9196 (mm) REVERT: B 288 LEU cc_start: 0.8984 (tt) cc_final: 0.8757 (pp) REVERT: B 295 MET cc_start: 0.9145 (tmm) cc_final: 0.8629 (tmm) REVERT: B 299 GLN cc_start: 0.9448 (mm-40) cc_final: 0.9073 (mm-40) REVERT: B 314 THR cc_start: 0.9203 (p) cc_final: 0.8928 (t) REVERT: B 326 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: B 355 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8806 (pp) outliers start: 43 outliers final: 35 residues processed: 229 average time/residue: 0.1697 time to fit residues: 56.9885 Evaluate side-chains 227 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8995 Z= 0.166 Angle : 0.751 10.206 12184 Z= 0.356 Chirality : 0.042 0.208 1469 Planarity : 0.004 0.045 1518 Dihedral : 7.921 80.268 1287 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 4.57 % Allowed : 32.12 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.53 (0.26), residues: 1133 helix: -0.27 (0.22), residues: 611 sheet: -0.48 (0.71), residues: 50 loop : -2.04 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 PHE 0.015 0.001 PHE B 115 TYR 0.012 0.001 TYR A 570 ARG 0.005 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.9081 (t80) cc_final: 0.8775 (t80) REVERT: A 191 ILE cc_start: 0.9496 (tp) cc_final: 0.9132 (tt) REVERT: A 262 LEU cc_start: 0.9547 (mm) cc_final: 0.9302 (mm) REVERT: A 290 LEU cc_start: 0.9402 (tp) cc_final: 0.8737 (pp) REVERT: A 295 MET cc_start: 0.8958 (tmm) cc_final: 0.8621 (tmm) REVERT: A 299 GLN cc_start: 0.9447 (mm-40) cc_final: 0.9060 (mm-40) REVERT: A 326 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: A 501 MET cc_start: 0.9128 (tpp) cc_final: 0.8752 (tpp) REVERT: B 122 GLU cc_start: 0.8637 (tt0) cc_final: 0.8361 (tt0) REVERT: B 145 PHE cc_start: 0.9244 (t80) cc_final: 0.8642 (t80) REVERT: B 162 MET cc_start: 0.7541 (tpp) cc_final: 0.7082 (tpp) REVERT: B 191 ILE cc_start: 0.9470 (tp) cc_final: 0.9139 (tt) REVERT: B 219 SER cc_start: 0.8101 (t) cc_final: 0.7593 (p) REVERT: B 243 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8885 (tm-30) REVERT: B 262 LEU cc_start: 0.9487 (mm) cc_final: 0.9188 (mm) REVERT: B 288 LEU cc_start: 0.8990 (tt) cc_final: 0.8755 (pp) REVERT: B 295 MET cc_start: 0.9178 (tmm) cc_final: 0.8674 (tmm) REVERT: B 299 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9088 (mm-40) REVERT: B 314 THR cc_start: 0.9312 (p) cc_final: 0.9089 (t) REVERT: B 326 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: B 355 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (pp) outliers start: 44 outliers final: 35 residues processed: 220 average time/residue: 0.1618 time to fit residues: 52.9324 Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 0.0270 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8995 Z= 0.161 Angle : 0.743 9.761 12184 Z= 0.350 Chirality : 0.042 0.201 1469 Planarity : 0.004 0.045 1518 Dihedral : 7.718 80.813 1287 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 3.64 % Allowed : 33.58 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.26), residues: 1133 helix: -0.23 (0.22), residues: 607 sheet: -0.42 (0.72), residues: 50 loop : -2.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.006 0.001 HIS A 535 PHE 0.007 0.001 PHE A 348 TYR 0.011 0.001 TYR B 408 ARG 0.007 0.000 ARG A 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8537 (tt0) cc_final: 0.8291 (tt0) REVERT: A 145 PHE cc_start: 0.9079 (t80) cc_final: 0.8799 (t80) REVERT: A 191 ILE cc_start: 0.9454 (tp) cc_final: 0.9082 (tt) REVERT: A 262 LEU cc_start: 0.9544 (mm) cc_final: 0.9288 (mm) REVERT: A 290 LEU cc_start: 0.9421 (tp) cc_final: 0.8754 (pp) REVERT: A 295 MET cc_start: 0.8969 (tmm) cc_final: 0.8633 (tmm) REVERT: A 299 GLN cc_start: 0.9443 (mm-40) cc_final: 0.9062 (mm-40) REVERT: A 326 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8258 (pp20) REVERT: A 388 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8671 (mm-30) REVERT: A 501 MET cc_start: 0.9070 (tpp) cc_final: 0.8675 (tpp) REVERT: B 122 GLU cc_start: 0.8613 (tt0) cc_final: 0.8371 (tt0) REVERT: B 145 PHE cc_start: 0.9248 (t80) cc_final: 0.8650 (t80) REVERT: B 162 MET cc_start: 0.7695 (tpp) cc_final: 0.7231 (tpp) REVERT: B 191 ILE cc_start: 0.9498 (tp) cc_final: 0.9148 (tt) REVERT: B 219 SER cc_start: 0.8074 (t) cc_final: 0.7547 (p) REVERT: B 243 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8881 (tm-30) REVERT: B 262 LEU cc_start: 0.9483 (mm) cc_final: 0.9168 (mm) REVERT: B 288 LEU cc_start: 0.9000 (tt) cc_final: 0.8771 (pp) REVERT: B 295 MET cc_start: 0.9222 (tmm) cc_final: 0.8735 (tmm) REVERT: B 299 GLN cc_start: 0.9420 (mm-40) cc_final: 0.9098 (mm-40) REVERT: B 314 THR cc_start: 0.9280 (p) cc_final: 0.8998 (t) REVERT: B 326 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8266 (pp20) REVERT: B 355 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8737 (pp) outliers start: 35 outliers final: 31 residues processed: 214 average time/residue: 0.1660 time to fit residues: 52.8599 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076668 restraints weight = 25947.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079793 restraints weight = 14459.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081976 restraints weight = 9765.472| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8995 Z= 0.165 Angle : 0.747 11.419 12184 Z= 0.352 Chirality : 0.042 0.204 1469 Planarity : 0.004 0.044 1518 Dihedral : 7.650 80.315 1287 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 3.64 % Allowed : 33.89 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.40 (0.26), residues: 1133 helix: -0.17 (0.22), residues: 608 sheet: -0.38 (0.73), residues: 50 loop : -1.98 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.003 0.001 HIS B 141 PHE 0.011 0.001 PHE B 115 TYR 0.011 0.001 TYR B 570 ARG 0.006 0.000 ARG A 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.95 seconds wall clock time: 35 minutes 23.78 seconds (2123.78 seconds total)