Starting phenix.real_space_refine on Sun Mar 17 14:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/03_2024/6lid_0904_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Ca 2 9.91 5 P 4 5.49 5 S 90 5.16 5 C 11548 2.51 5 N 2824 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "C" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 10.08, per 1000 atoms: 0.56 Number of scatterers: 17964 At special positions: 0 Unit cell: (81.825, 138.557, 138.557, 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) Ca 2 19.99 S 90 16.00 P 4 15.00 O 3496 8.00 N 2824 7.00 C 11548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS B 144 " distance=2.86 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS D 144 " distance=2.95 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 332 " " NAG G 1 " - " ASN A 495 " " NAG H 1 " - " ASN A 513 " " NAG I 1 " - " ASN A 575 " " NAG J 1 " - " ASN C 261 " " NAG K 1 " - " ASN C 332 " " NAG L 1 " - " ASN C 495 " " NAG M 1 " - " ASN C 513 " " NAG N 1 " - " ASN C 575 " Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.2 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 12 sheets defined 47.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 80 through 110 removed outlier: 3.581A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.841A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.558A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASP A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.619A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.980A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.936A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.176A pdb=" N MET A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR A 397 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.544A pdb=" N VAL A 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.837A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.514A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.649A pdb=" N GLU B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.806A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.519A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 177 through 201 removed outlier: 3.607A pdb=" N LYS B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 230 removed outlier: 3.621A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 251 through 277 Proline residue: B 261 - end of helix removed outlier: 4.168A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.709A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.989A pdb=" N VAL B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Proline residue: B 306 - end of helix removed outlier: 4.428A pdb=" N VAL B 309 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 311 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 313 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 319 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.507A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.869A pdb=" N ILE B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 375 through 397 removed outlier: 3.847A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.511A pdb=" N SER B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.726A pdb=" N GLY B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 Proline residue: B 468 - end of helix removed outlier: 3.510A pdb=" N MET B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.606A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 80 through 110 removed outlier: 3.581A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.841A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.557A pdb=" N LYS C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.619A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.980A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 290 through 306 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.936A pdb=" N GLN C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.177A pdb=" N MET C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 397 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 434 Processing helix chain 'C' and resid 453 through 456 No H-bonds generated for 'chain 'C' and resid 453 through 456' Processing helix chain 'C' and resid 459 through 471 removed outlier: 3.544A pdb=" N VAL C 462 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN C 463 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 464 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 465 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 467 " --> pdb=" O VAL C 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 468 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 470 " --> pdb=" O MET C 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 471 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 515 through 518 Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 548 through 561 Processing helix chain 'C' and resid 563 through 566 No H-bonds generated for 'chain 'C' and resid 563 through 566' Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 663 through 665 No H-bonds generated for 'chain 'C' and resid 663 through 665' Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.837A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.506A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 62 through 90 removed outlier: 3.513A pdb=" N ILE D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.649A pdb=" N GLU D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.806A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.518A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 177 through 201 removed outlier: 3.606A pdb=" N LYS D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.621A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 251 through 277 Proline residue: D 261 - end of helix removed outlier: 4.168A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.709A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 302 through 321 removed outlier: 3.989A pdb=" N VAL D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Proline residue: D 306 - end of helix removed outlier: 4.428A pdb=" N VAL D 309 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 311 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 314 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 315 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 318 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 319 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.507A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 368 removed outlier: 3.869A pdb=" N ILE D 367 " --> pdb=" O THR D 363 " (cutoff:3.500A) Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 375 through 397 removed outlier: 3.848A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 431 removed outlier: 3.510A pdb=" N SER D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 441 through 454 removed outlier: 3.727A pdb=" N GLY D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 477 Proline residue: D 468 - end of helix removed outlier: 3.511A pdb=" N MET D 475 " --> pdb=" O MET D 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.544A pdb=" N THR A 475 " --> pdb=" O TRP A 443 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR A 124 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 126 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 162 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE A 162 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 208 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 310 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE A 211 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 312 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 380 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 313 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY A 382 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.536A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 569 through 572 removed outlier: 6.588A pdb=" N GLU A 649 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 620 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 605 Processing sheet with id= E, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= F, first strand: chain 'A' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE A 680 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 442 through 444 removed outlier: 6.544A pdb=" N THR C 475 " --> pdb=" O TRP C 443 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR C 124 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL C 160 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 126 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 162 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 206 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 162 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 208 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C 310 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE C 211 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER C 312 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 380 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 313 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY C 382 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.537A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 569 through 572 removed outlier: 6.587A pdb=" N GLU C 649 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 620 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 603 through 605 Processing sheet with id= K, first strand: chain 'C' and resid 617 through 619 Processing sheet with id= L, first strand: chain 'C' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE C 680 " --> pdb=" O SER C 675 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1584 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: 5.53 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4702 1.33 - 1.45: 3458 1.45 - 1.57: 9862 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 18172 Sorted by residual: bond pdb=" C31 3PH B 702 " pdb=" O31 3PH B 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C31 3PH D 702 " pdb=" O31 3PH D 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 3PH B 701 " pdb=" O31 3PH B 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 3PH D 701 " pdb=" O21 3PH D 701 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 701 " pdb=" O31 3PH D 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18167 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.05: 452 106.05 - 113.16: 9747 113.16 - 120.26: 7316 120.26 - 127.37: 6949 127.37 - 134.48: 232 Bond angle restraints: 24696 Sorted by residual: angle pdb=" N GLU D 484 " pdb=" CA GLU D 484 " pdb=" C GLU D 484 " ideal model delta sigma weight residual 108.74 118.65 -9.91 1.38e+00 5.25e-01 5.16e+01 angle pdb=" N TYR A 175 " pdb=" CA TYR A 175 " pdb=" C TYR A 175 " ideal model delta sigma weight residual 110.91 118.92 -8.01 1.17e+00 7.31e-01 4.69e+01 angle pdb=" N TYR C 175 " pdb=" CA TYR C 175 " pdb=" C TYR C 175 " ideal model delta sigma weight residual 110.91 118.88 -7.97 1.17e+00 7.31e-01 4.64e+01 angle pdb=" N ILE D 465 " pdb=" CA ILE D 465 " pdb=" C ILE D 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.37e+01 angle pdb=" N ILE B 465 " pdb=" CA ILE B 465 " pdb=" C ILE B 465 " ideal model delta sigma weight residual 111.90 106.55 5.35 8.10e-01 1.52e+00 4.36e+01 ... (remaining 24691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 10328 23.96 - 47.93: 548 47.93 - 71.89: 93 71.89 - 95.85: 19 95.85 - 119.81: 2 Dihedral angle restraints: 10990 sinusoidal: 4674 harmonic: 6316 Sorted by residual: dihedral pdb=" CA TYR A 259 " pdb=" C TYR A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA TYR C 259 " pdb=" C TYR C 259 " pdb=" N GLY C 260 " pdb=" CA GLY C 260 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 114 " pdb=" SG CYS C 114 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 134.07 -41.07 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 10987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2768 0.146 - 0.293: 36 0.293 - 0.439: 10 0.439 - 0.585: 0 0.585 - 0.732: 4 Chirality restraints: 2818 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 513 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 2815 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 261 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 260 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO D 261 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 428 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.038 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 158 2.49 - 3.09: 11164 3.09 - 3.70: 27417 3.70 - 4.30: 43634 4.30 - 4.90: 67753 Nonbonded interactions: 150126 Sorted by model distance: nonbonded pdb=" ND1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 1.890 3.420 nonbonded pdb=" ND1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 1.894 3.420 nonbonded pdb=" CE1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 2.208 3.560 nonbonded pdb=" O PRO B 482 " pdb=" N GLU B 484 " model vdw 2.238 2.520 nonbonded pdb=" CE1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 2.238 3.560 ... (remaining 150121 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.100 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 50.200 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.007 0.125 18172 Z= 0.476 Angle : 0.995 9.912 24696 Z= 0.528 Chirality : 0.064 0.732 2818 Planarity : 0.007 0.081 3056 Dihedral : 15.030 119.812 6924 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 3.17 % Favored : 94.87 % 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: -4.84 (0.13), residues: 2154 helix: -4.66 (0.05), residues: 998 sheet: -0.33 (0.34), residues: 182 loop : -1.96 (0.16), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 383 HIS 0.007 0.001 HIS C 348 PHE 0.023 0.002 PHE A 407 TYR 0.022 0.002 TYR C 65 ARG 0.004 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 343 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8566 (tmm) REVERT: A 381 MET cc_start: 0.8748 (ttp) cc_final: 0.8385 (ttp) REVERT: A 432 MET cc_start: 0.9225 (mmm) cc_final: 0.9000 (mmp) REVERT: A 435 MET cc_start: 0.9140 (ptt) cc_final: 0.8845 (ptt) REVERT: B 116 SER cc_start: 0.7218 (OUTLIER) cc_final: 0.6721 (m) REVERT: B 468 PRO cc_start: 0.5965 (Cg_exo) cc_final: 0.5617 (Cg_endo) REVERT: C 357 MET cc_start: 0.8938 (tmm) cc_final: 0.8567 (tmm) REVERT: C 381 MET cc_start: 0.8747 (ttp) cc_final: 0.8380 (ttp) REVERT: C 432 MET cc_start: 0.9234 (mmm) cc_final: 0.9000 (mmp) REVERT: C 435 MET cc_start: 0.9146 (ptt) cc_final: 0.8850 (ptt) REVERT: D 116 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6571 (m) REVERT: D 194 SER cc_start: 0.7013 (p) cc_final: 0.6473 (m) outliers start: 37 outliers final: 4 residues processed: 368 average time/residue: 1.1173 time to fit residues: 467.2951 Evaluate side-chains 205 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 145 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 156 ASN A 201 HIS A 220 HIS A 324 HIS A 330 GLN A 422 ASN A 442 ASN A 493 ASN A 510 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 606 ASN A 609 ASN A 625 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN C 125 GLN C 156 ASN C 201 HIS C 220 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS C 330 GLN C 422 ASN C 442 ASN C 493 ASN C 510 GLN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN C 606 ASN C 609 ASN C 625 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 474 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 18172 Z= 0.426 Angle : 0.835 10.210 24696 Z= 0.419 Chirality : 0.057 0.508 2818 Planarity : 0.007 0.051 3056 Dihedral : 11.873 111.824 2962 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.28 % Allowed : 10.36 % Favored : 86.36 % 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: -2.75 (0.15), residues: 2154 helix: -2.29 (0.13), residues: 974 sheet: -0.00 (0.35), residues: 182 loop : -1.55 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 239 HIS 0.010 0.002 HIS A 348 PHE 0.026 0.003 PHE C 407 TYR 0.019 0.002 TYR D 97 ARG 0.008 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 219 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 280 LYS cc_start: 0.8694 (pttp) cc_final: 0.8395 (ptpt) REVERT: A 435 MET cc_start: 0.9288 (ptt) cc_final: 0.8971 (ptt) REVERT: A 523 SER cc_start: 0.8679 (m) cc_final: 0.8459 (t) REVERT: A 542 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8652 (mtpt) REVERT: B 180 PHE cc_start: 0.5762 (m-10) cc_final: 0.5554 (m-10) REVERT: B 181 THR cc_start: 0.6956 (OUTLIER) cc_final: 0.6755 (p) REVERT: B 194 SER cc_start: 0.7226 (p) cc_final: 0.6858 (m) REVERT: B 337 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5650 (tpt) REVERT: B 423 PHE cc_start: 0.5530 (t80) cc_final: 0.5088 (t80) REVERT: B 453 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.4935 (tp) REVERT: C 271 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8194 (t0) REVERT: C 280 LYS cc_start: 0.8696 (pttp) cc_final: 0.8397 (ptpt) REVERT: C 435 MET cc_start: 0.9293 (ptt) cc_final: 0.8972 (ptt) REVERT: C 523 SER cc_start: 0.8692 (m) cc_final: 0.8482 (t) REVERT: C 542 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8667 (mtpt) REVERT: C 585 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: D 180 PHE cc_start: 0.5383 (m-10) cc_final: 0.5173 (m-10) REVERT: D 194 SER cc_start: 0.7048 (p) cc_final: 0.6682 (m) REVERT: D 464 LYS cc_start: 0.4326 (OUTLIER) cc_final: 0.3437 (mmtm) outliers start: 62 outliers final: 24 residues processed: 261 average time/residue: 1.1866 time to fit residues: 349.9571 Evaluate side-chains 222 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 609 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 609 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18172 Z= 0.220 Angle : 0.686 9.856 24696 Z= 0.334 Chirality : 0.049 0.382 2818 Planarity : 0.005 0.043 3056 Dihedral : 11.375 112.311 2952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.28 % Allowed : 12.47 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.17), residues: 2154 helix: -0.91 (0.15), residues: 978 sheet: -0.03 (0.36), residues: 180 loop : -1.32 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 239 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE C 407 TYR 0.016 0.001 TYR C 259 ARG 0.004 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 216 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8266 (t0) REVERT: A 435 MET cc_start: 0.9259 (ptt) cc_final: 0.8980 (ptt) REVERT: A 465 MET cc_start: 0.8969 (mmm) cc_final: 0.8704 (mmm) REVERT: A 512 ASP cc_start: 0.7212 (p0) cc_final: 0.6865 (p0) REVERT: B 134 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 180 PHE cc_start: 0.5856 (m-10) cc_final: 0.5602 (m-10) REVERT: B 194 SER cc_start: 0.7144 (p) cc_final: 0.6852 (m) REVERT: B 254 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.4948 (tp) REVERT: B 282 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: B 402 GLU cc_start: 0.5805 (mp0) cc_final: 0.4189 (tp30) REVERT: B 423 PHE cc_start: 0.5550 (t80) cc_final: 0.4805 (t80) REVERT: C 271 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8264 (t0) REVERT: C 435 MET cc_start: 0.9261 (ptt) cc_final: 0.8979 (ptt) REVERT: C 465 MET cc_start: 0.8966 (mmm) cc_final: 0.8701 (mmm) REVERT: C 512 ASP cc_start: 0.7209 (p0) cc_final: 0.6864 (p0) REVERT: D 134 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 180 PHE cc_start: 0.5408 (m-10) cc_final: 0.5195 (m-10) REVERT: D 181 THR cc_start: 0.6664 (OUTLIER) cc_final: 0.6350 (p) REVERT: D 194 SER cc_start: 0.6871 (p) cc_final: 0.6559 (m) REVERT: D 263 VAL cc_start: 0.6275 (OUTLIER) cc_final: 0.5759 (p) REVERT: D 360 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 442 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6302 (mt) REVERT: D 464 LYS cc_start: 0.4117 (OUTLIER) cc_final: 0.3256 (mmtm) outliers start: 62 outliers final: 18 residues processed: 256 average time/residue: 1.2079 time to fit residues: 349.5445 Evaluate side-chains 221 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 679 ASN B 206 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18172 Z= 0.336 Angle : 0.749 10.203 24696 Z= 0.367 Chirality : 0.053 0.451 2818 Planarity : 0.005 0.047 3056 Dihedral : 11.301 116.042 2948 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.86 % Allowed : 13.53 % Favored : 82.61 % 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: -1.11 (0.17), residues: 2154 helix: -0.34 (0.16), residues: 978 sheet: -0.00 (0.36), residues: 182 loop : -1.20 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 239 HIS 0.008 0.002 HIS A 348 PHE 0.023 0.002 PHE C 407 TYR 0.021 0.002 TYR C 259 ARG 0.005 0.001 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 207 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: A 271 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 435 MET cc_start: 0.9296 (ptt) cc_final: 0.9014 (ptt) REVERT: A 512 ASP cc_start: 0.7617 (p0) cc_final: 0.7153 (p0) REVERT: A 585 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 610 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8144 (mmt) REVERT: A 653 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7992 (mtpt) REVERT: B 134 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 194 SER cc_start: 0.7267 (p) cc_final: 0.7013 (m) REVERT: B 254 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.4868 (tp) REVERT: B 276 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7469 (t) REVERT: B 282 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: B 402 GLU cc_start: 0.5729 (mp0) cc_final: 0.4215 (tp30) REVERT: C 271 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8352 (t0) REVERT: C 435 MET cc_start: 0.9301 (ptt) cc_final: 0.9015 (ptt) REVERT: C 512 ASP cc_start: 0.7615 (p0) cc_final: 0.7151 (p0) REVERT: C 585 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 610 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8109 (mmt) REVERT: D 101 MET cc_start: 0.6820 (ppp) cc_final: 0.6372 (pp-130) REVERT: D 134 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: D 180 PHE cc_start: 0.5481 (m-10) cc_final: 0.5278 (m-10) REVERT: D 194 SER cc_start: 0.6910 (p) cc_final: 0.6629 (m) REVERT: D 263 VAL cc_start: 0.6114 (OUTLIER) cc_final: 0.5643 (p) REVERT: D 276 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7346 (t) REVERT: D 442 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6195 (mt) REVERT: D 464 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3389 (mmtm) outliers start: 73 outliers final: 32 residues processed: 257 average time/residue: 1.2080 time to fit residues: 349.7553 Evaluate side-chains 237 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18172 Z= 0.182 Angle : 0.656 10.291 24696 Z= 0.315 Chirality : 0.048 0.359 2818 Planarity : 0.004 0.046 3056 Dihedral : 10.840 112.030 2948 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.85 % Allowed : 14.53 % Favored : 82.61 % 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: -0.62 (0.18), residues: 2154 helix: 0.11 (0.17), residues: 978 sheet: 0.10 (0.36), residues: 182 loop : -0.97 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 230 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE C 407 TYR 0.016 0.001 TYR C 259 ARG 0.006 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 210 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8316 (t0) REVERT: A 432 MET cc_start: 0.9115 (mmm) cc_final: 0.8903 (mmp) REVERT: A 512 ASP cc_start: 0.7213 (p0) cc_final: 0.6844 (p0) REVERT: A 653 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7925 (mtpt) REVERT: B 85 GLU cc_start: 0.6069 (tm-30) cc_final: 0.5305 (pt0) REVERT: B 194 SER cc_start: 0.7058 (p) cc_final: 0.6763 (m) REVERT: B 254 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.4951 (tp) REVERT: B 282 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: B 365 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: B 393 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4803 (tp) REVERT: B 402 GLU cc_start: 0.5665 (mp0) cc_final: 0.4187 (tp30) REVERT: B 442 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6066 (mt) REVERT: B 453 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.4949 (tp) REVERT: C 271 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 432 MET cc_start: 0.9119 (mmm) cc_final: 0.8903 (mmp) REVERT: C 512 ASP cc_start: 0.7215 (p0) cc_final: 0.6844 (p0) REVERT: C 653 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7922 (mtpt) REVERT: D 101 MET cc_start: 0.6744 (ppp) cc_final: 0.6498 (pp-130) REVERT: D 134 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: D 180 PHE cc_start: 0.5615 (m-10) cc_final: 0.5360 (m-10) REVERT: D 194 SER cc_start: 0.6884 (p) cc_final: 0.6643 (m) REVERT: D 263 VAL cc_start: 0.6179 (OUTLIER) cc_final: 0.5629 (p) REVERT: D 270 MET cc_start: 0.7032 (mmm) cc_final: 0.6830 (mmm) REVERT: D 442 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6183 (mt) REVERT: D 464 LYS cc_start: 0.4215 (OUTLIER) cc_final: 0.3434 (mmtm) outliers start: 54 outliers final: 20 residues processed: 249 average time/residue: 1.1946 time to fit residues: 335.8298 Evaluate side-chains 226 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.7980 chunk 186 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18172 Z= 0.152 Angle : 0.629 10.216 24696 Z= 0.299 Chirality : 0.047 0.344 2818 Planarity : 0.004 0.049 3056 Dihedral : 10.488 109.917 2948 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.96 % Allowed : 15.38 % Favored : 81.66 % 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: -0.29 (0.18), residues: 2154 helix: 0.48 (0.17), residues: 972 sheet: 0.18 (0.37), residues: 182 loop : -0.87 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 230 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE C 407 TYR 0.015 0.001 TYR C 259 ARG 0.007 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8237 (t0) REVERT: A 432 MET cc_start: 0.9089 (mmm) cc_final: 0.8869 (mmp) REVERT: A 512 ASP cc_start: 0.7063 (p0) cc_final: 0.6627 (p0) REVERT: A 653 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7881 (mtpt) REVERT: B 254 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.4904 (tp) REVERT: B 282 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: B 365 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7322 (m-10) REVERT: B 402 GLU cc_start: 0.5669 (mp0) cc_final: 0.4191 (tp30) REVERT: B 442 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6069 (mt) REVERT: B 453 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4916 (tp) REVERT: C 271 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8238 (t0) REVERT: C 432 MET cc_start: 0.9087 (mmm) cc_final: 0.8875 (mmp) REVERT: C 512 ASP cc_start: 0.7066 (p0) cc_final: 0.6627 (p0) REVERT: C 653 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7875 (mtpt) REVERT: D 134 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 180 PHE cc_start: 0.5600 (m-10) cc_final: 0.5367 (m-10) REVERT: D 194 SER cc_start: 0.6841 (p) cc_final: 0.6635 (m) REVERT: D 263 VAL cc_start: 0.6180 (OUTLIER) cc_final: 0.5623 (p) REVERT: D 380 PHE cc_start: 0.6609 (t80) cc_final: 0.6392 (t80) REVERT: D 442 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6158 (mt) REVERT: D 464 LYS cc_start: 0.4343 (OUTLIER) cc_final: 0.4012 (mmtp) outliers start: 56 outliers final: 18 residues processed: 236 average time/residue: 1.2396 time to fit residues: 329.1319 Evaluate side-chains 220 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 129 optimal weight: 0.0870 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18172 Z= 0.161 Angle : 0.633 10.219 24696 Z= 0.301 Chirality : 0.047 0.356 2818 Planarity : 0.004 0.050 3056 Dihedral : 10.313 108.916 2948 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.22 % Allowed : 15.54 % Favored : 81.24 % 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: -0.15 (0.18), residues: 2154 helix: 0.63 (0.17), residues: 966 sheet: 0.20 (0.37), residues: 182 loop : -0.83 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 230 HIS 0.004 0.001 HIS C 348 PHE 0.016 0.001 PHE C 407 TYR 0.015 0.001 TYR A 259 ARG 0.006 0.000 ARG C 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 191 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8212 (t0) REVERT: A 512 ASP cc_start: 0.7101 (p0) cc_final: 0.6674 (p0) REVERT: A 653 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7922 (mtpt) REVERT: B 254 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.4934 (tp) REVERT: B 282 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: B 323 THR cc_start: 0.5751 (OUTLIER) cc_final: 0.5486 (p) REVERT: B 365 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: B 402 GLU cc_start: 0.5762 (mp0) cc_final: 0.4217 (tp30) REVERT: B 423 PHE cc_start: 0.5687 (t80) cc_final: 0.5092 (t80) REVERT: B 442 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6073 (mt) REVERT: B 453 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.4848 (tp) REVERT: C 271 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8210 (t0) REVERT: C 512 ASP cc_start: 0.7103 (p0) cc_final: 0.6674 (p0) REVERT: C 653 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7915 (mtpt) REVERT: D 134 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 194 SER cc_start: 0.6977 (p) cc_final: 0.6751 (m) REVERT: D 263 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.5754 (p) REVERT: D 323 THR cc_start: 0.5640 (OUTLIER) cc_final: 0.5292 (p) REVERT: D 442 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6155 (mt) REVERT: D 464 LYS cc_start: 0.4278 (OUTLIER) cc_final: 0.3994 (mmtp) outliers start: 61 outliers final: 27 residues processed: 238 average time/residue: 1.1525 time to fit residues: 311.0724 Evaluate side-chains 225 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 162 optimal weight: 10.0000 chunk 187 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18172 Z= 0.152 Angle : 0.615 9.765 24696 Z= 0.292 Chirality : 0.046 0.346 2818 Planarity : 0.004 0.052 3056 Dihedral : 10.149 107.527 2948 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.01 % Allowed : 15.86 % Favored : 81.13 % 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: -0.03 (0.18), residues: 2154 helix: 0.71 (0.17), residues: 972 sheet: 0.25 (0.37), residues: 182 loop : -0.75 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 383 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE B 180 TYR 0.014 0.001 TYR A 259 ARG 0.008 0.000 ARG C 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8216 (t0) REVERT: A 512 ASP cc_start: 0.7031 (p0) cc_final: 0.6627 (p0) REVERT: A 653 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7917 (mtpt) REVERT: B 254 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.4964 (tp) REVERT: B 323 THR cc_start: 0.5791 (OUTLIER) cc_final: 0.5553 (p) REVERT: B 365 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: B 402 GLU cc_start: 0.5757 (mp0) cc_final: 0.4230 (tp30) REVERT: B 442 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6068 (mt) REVERT: C 271 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8229 (t0) REVERT: C 512 ASP cc_start: 0.7032 (p0) cc_final: 0.6614 (p0) REVERT: C 653 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7911 (mtpt) REVERT: D 134 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: D 194 SER cc_start: 0.6961 (p) cc_final: 0.6699 (m) REVERT: D 263 VAL cc_start: 0.6351 (OUTLIER) cc_final: 0.5839 (p) REVERT: D 323 THR cc_start: 0.5633 (OUTLIER) cc_final: 0.5295 (p) REVERT: D 442 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6078 (mt) REVERT: D 464 LYS cc_start: 0.4439 (OUTLIER) cc_final: 0.4069 (mmtp) outliers start: 57 outliers final: 23 residues processed: 237 average time/residue: 1.2116 time to fit residues: 323.8307 Evaluate side-chains 224 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 3.9990 chunk 180 optimal weight: 0.0050 chunk 192 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 191 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18172 Z= 0.168 Angle : 0.629 11.347 24696 Z= 0.299 Chirality : 0.047 0.355 2818 Planarity : 0.004 0.053 3056 Dihedral : 10.112 107.491 2948 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.59 % Allowed : 16.49 % Favored : 80.92 % 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: 0.01 (0.18), residues: 2154 helix: 0.79 (0.17), residues: 970 sheet: 0.24 (0.37), residues: 182 loop : -0.76 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.005 0.001 HIS A 348 PHE 0.020 0.001 PHE D 180 TYR 0.016 0.001 TYR A 259 ARG 0.009 0.000 ARG C 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8221 (t0) REVERT: A 512 ASP cc_start: 0.7125 (p0) cc_final: 0.6654 (p0) REVERT: A 653 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7923 (mtpt) REVERT: B 254 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.4978 (tp) REVERT: B 323 THR cc_start: 0.5703 (OUTLIER) cc_final: 0.5458 (p) REVERT: B 365 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: B 402 GLU cc_start: 0.5811 (mp0) cc_final: 0.4103 (tp30) REVERT: B 442 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6139 (mt) REVERT: C 271 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8216 (t0) REVERT: C 512 ASP cc_start: 0.7130 (p0) cc_final: 0.6664 (p0) REVERT: C 653 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7918 (mtpt) REVERT: D 134 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: D 263 VAL cc_start: 0.6322 (OUTLIER) cc_final: 0.5799 (p) REVERT: D 323 THR cc_start: 0.5651 (OUTLIER) cc_final: 0.5317 (p) REVERT: D 442 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6237 (mt) REVERT: D 464 LYS cc_start: 0.4331 (OUTLIER) cc_final: 0.4084 (mmtp) outliers start: 49 outliers final: 25 residues processed: 231 average time/residue: 1.2731 time to fit residues: 331.8240 Evaluate side-chains 225 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 131 optimal weight: 0.0030 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18172 Z= 0.155 Angle : 0.620 12.285 24696 Z= 0.294 Chirality : 0.046 0.345 2818 Planarity : 0.004 0.058 3056 Dihedral : 10.020 106.726 2948 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.38 % Allowed : 16.97 % Favored : 80.66 % 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: 0.08 (0.18), residues: 2154 helix: 0.86 (0.17), residues: 970 sheet: 0.27 (0.37), residues: 182 loop : -0.75 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.001 PHE B 180 TYR 0.014 0.001 TYR A 259 ARG 0.005 0.000 ARG A 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8231 (t0) REVERT: A 512 ASP cc_start: 0.7032 (p0) cc_final: 0.6590 (p0) REVERT: A 653 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7919 (mtpt) REVERT: B 254 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5031 (tp) REVERT: B 323 THR cc_start: 0.5888 (OUTLIER) cc_final: 0.5606 (p) REVERT: B 365 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7369 (m-10) REVERT: B 402 GLU cc_start: 0.5852 (mp0) cc_final: 0.4199 (tp30) REVERT: B 423 PHE cc_start: 0.5917 (t80) cc_final: 0.5622 (t80) REVERT: B 442 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6076 (mt) REVERT: C 271 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8232 (t0) REVERT: C 512 ASP cc_start: 0.7033 (p0) cc_final: 0.6590 (p0) REVERT: C 653 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7913 (mtpt) REVERT: D 263 VAL cc_start: 0.6303 (OUTLIER) cc_final: 0.5780 (p) REVERT: D 323 THR cc_start: 0.5616 (OUTLIER) cc_final: 0.5283 (p) REVERT: D 442 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6159 (mt) REVERT: D 464 LYS cc_start: 0.4276 (OUTLIER) cc_final: 0.4041 (mmtp) outliers start: 45 outliers final: 26 residues processed: 225 average time/residue: 1.2904 time to fit residues: 326.8741 Evaluate side-chains 223 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 653 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 464 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114593 restraints weight = 19349.563| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.71 r_work: 0.2955 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18172 Z= 0.175 Angle : 0.625 11.866 24696 Z= 0.299 Chirality : 0.047 0.355 2818 Planarity : 0.004 0.054 3056 Dihedral : 10.037 107.348 2948 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.54 % Allowed : 16.91 % Favored : 80.55 % 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: 0.09 (0.18), residues: 2154 helix: 0.89 (0.17), residues: 976 sheet: 0.24 (0.37), residues: 182 loop : -0.77 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.005 0.001 HIS C 348 PHE 0.024 0.001 PHE D 180 TYR 0.016 0.001 TYR C 259 ARG 0.006 0.000 ARG C 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6317.48 seconds wall clock time: 112 minutes 36.69 seconds (6756.69 seconds total)