Starting phenix.real_space_refine on Thu Feb 15 02:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2024/7c7s_30301_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 Cl 2 4.86 5 C 7062 2.51 5 N 1798 2.21 5 O 1991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 831": "OD1" <-> "OD2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ASP 688": "OD1" <-> "OD2" Residue "B PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 748": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10915 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5457 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 28, 'TRANS': 656} Chain breaks: 2 Chain: "B" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5321 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 28, 'TRANS': 641} Chain breaks: 3 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {'2BV': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.14, per 1000 atoms: 0.56 Number of scatterers: 10915 At special positions: 0 Unit cell: (78.078, 103.428, 172.38, 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) Cl 2 17.00 S 61 16.00 P 1 15.00 O 1991 8.00 N 1798 7.00 C 7062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.23 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.17 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 NAG-ASN " NAG A1001 " - " ASN A 409 " " NAG A1002 " - " ASN A 440 " " NAG A1003 " - " ASN A 482 " " NAG A1004 " - " ASN A 502 " " NAG A1005 " - " ASN A 514 " " NAG B1001 " - " ASN B 389 " " NAG B1002 " - " ASN B 404 " " NAG B1003 " - " ASN B 453 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 10 sheets defined 49.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.93 Creating SS restraints... Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.000A pdb=" N CYS A 188 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLN A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Proline residue: A 190 - end of helix removed outlier: 3.821A pdb=" N MET A 194 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 4.004A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 removed outlier: 4.727A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.646A pdb=" N HIS A 293 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Proline residue: A 295 - end of helix removed outlier: 3.776A pdb=" N VAL A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 302 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.741A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.657A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 464 through 484 removed outlier: 3.534A pdb=" N ALA A 467 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Proline residue: A 468 - end of helix removed outlier: 3.586A pdb=" N THR A 484 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 589 through 615 Processing helix chain 'A' and resid 627 through 648 removed outlier: 4.327A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 659 through 692 removed outlier: 3.966A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 removed outlier: 3.846A pdb=" N VAL A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 790 removed outlier: 3.531A pdb=" N ILE A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 825 removed outlier: 4.015A pdb=" N MET A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 821 - end of helix removed outlier: 3.910A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 861 Proline residue: A 855 - end of helix removed outlier: 4.782A pdb=" N LEU A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.596A pdb=" N SER B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 136 through 149 removed outlier: 3.644A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 179 through 193 removed outlier: 4.029A pdb=" N VAL B 182 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 183 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.771A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.694A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 479 through 505 Processing helix chain 'B' and resid 510 through 513 No H-bonds generated for 'chain 'B' and resid 510 through 513' Processing helix chain 'B' and resid 517 through 538 removed outlier: 4.047A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 553 through 583 removed outlier: 3.711A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 618 Processing helix chain 'B' and resid 653 through 677 removed outlier: 3.712A pdb=" N LEU B 667 " --> pdb=" O TYR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 712 Processing helix chain 'B' and resid 717 through 740 Processing helix chain 'B' and resid 742 through 748 removed outlier: 4.386A pdb=" N LEU B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 209 through 217 removed outlier: 6.395A pdb=" N ARG A 168 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS A 212 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 170 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 214 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 172 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS A 216 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 174 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLY A 173 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 242 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 175 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= C, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.474A pdb=" N VAL A 389 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 423 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN A 541 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS A 549 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.547A pdb=" N PHE A 518 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 580 through 584 removed outlier: 7.063A pdb=" N SER A 753 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 583 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 755 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.730A pdb=" N GLU A 336 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR A 311 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR A 338 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 12.159A pdb=" N GLN A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N ARG A 340 " --> pdb=" O GLN A 313 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 98 through 105 removed outlier: 7.267A pdb=" N MET B 59 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 130 " --> pdb=" O MET B 59 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 61 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY B 132 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 152 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY B 132 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU B 154 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 448 through 451 removed outlier: 3.741A pdb=" N ARG B 435 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU B 225 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR B 200 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER B 227 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 12.161A pdb=" N THR B 202 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N THR B 229 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 407 through 410 Processing sheet with id= J, first strand: chain 'B' and resid 622 through 627 511 hydrogen bonds defined for protein. 1398 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: 3.12 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3404 1.34 - 1.47: 2775 1.47 - 1.59: 4890 1.59 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 11170 Sorted by residual: bond pdb=" C5 2BV A1006 " pdb=" C6 2BV A1006 " ideal model delta sigma weight residual 1.394 1.486 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C VAL A 619 " pdb=" N ARG A 620 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.35e-02 5.49e+03 1.58e+01 bond pdb=" O2 2BV A1006 " pdb=" P 2BV A1006 " ideal model delta sigma weight residual 1.510 1.588 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N LEU B 621 " pdb=" CA LEU B 621 " ideal model delta sigma weight residual 1.457 1.418 0.039 1.30e-02 5.92e+03 9.21e+00 bond pdb=" O1 2BV A1006 " pdb=" P 2BV A1006 " ideal model delta sigma weight residual 1.528 1.471 0.057 2.00e-02 2.50e+03 8.23e+00 ... (remaining 11165 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 263 106.26 - 113.21: 6150 113.21 - 120.16: 4246 120.16 - 127.12: 4359 127.12 - 134.07: 134 Bond angle restraints: 15152 Sorted by residual: angle pdb=" C LEU B 539 " pdb=" N ASP B 540 " pdb=" CA ASP B 540 " ideal model delta sigma weight residual 120.31 127.44 -7.13 1.52e+00 4.33e-01 2.20e+01 angle pdb=" C PHE B 537 " pdb=" N GLY B 538 " pdb=" CA GLY B 538 " ideal model delta sigma weight residual 120.14 125.19 -5.05 1.25e+00 6.40e-01 1.63e+01 angle pdb=" N THR B 468 " pdb=" CA THR B 468 " pdb=" C THR B 468 " ideal model delta sigma weight residual 110.20 104.16 6.04 1.58e+00 4.01e-01 1.46e+01 angle pdb=" N ASN A 502 " pdb=" CA ASN A 502 " pdb=" CB ASN A 502 " ideal model delta sigma weight residual 109.95 115.74 -5.79 1.55e+00 4.16e-01 1.40e+01 angle pdb=" O1 2BV A1006 " pdb=" P 2BV A1006 " pdb=" O2 2BV A1006 " ideal model delta sigma weight residual 117.58 106.48 11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 15147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6307 21.38 - 42.75: 383 42.75 - 64.13: 49 64.13 - 85.51: 10 85.51 - 106.89: 8 Dihedral angle restraints: 6757 sinusoidal: 2820 harmonic: 3937 Sorted by residual: dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 410 " pdb=" CB CYS A 410 " ideal model delta sinusoidal sigma weight residual -86.00 -151.12 65.12 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS B 265 " pdb=" SG CYS B 265 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual -86.00 -146.78 60.78 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -146.70 60.70 1 1.00e+01 1.00e-02 4.90e+01 ... (remaining 6754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1526 0.076 - 0.153: 195 0.153 - 0.229: 9 0.229 - 0.306: 3 0.306 - 0.382: 2 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C2 2BV A1006 " pdb=" N 2BV A1006 " pdb=" C1 2BV A1006 " pdb=" C3 2BV A1006 " both_signs ideal model delta sigma weight residual False -2.51 -2.13 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 389 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 502 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1732 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 475 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG B 475 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG B 475 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 476 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 681 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C MET A 681 " 0.064 2.00e-02 2.50e+03 pdb=" O MET A 681 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A 682 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 190 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C PRO A 190 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO A 190 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA A 191 " -0.018 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 352 2.70 - 3.25: 11132 3.25 - 3.80: 17185 3.80 - 4.35: 21981 4.35 - 4.90: 36620 Nonbonded interactions: 87270 Sorted by model distance: nonbonded pdb=" NH1 ARG B 212 " pdb=" OG1 THR B 216 " model vdw 2.153 2.520 nonbonded pdb=" O PRO B 136 " pdb=" OG SER B 140 " model vdw 2.210 2.440 nonbonded pdb=" O CYS A 246 " pdb=" OG SER A 250 " model vdw 2.258 2.440 nonbonded pdb=" O LEU B 471 " pdb=" N ARG B 642 " model vdw 2.262 2.520 nonbonded pdb=" OG SER A 625 " pdb=" OD2 ASP A 801 " model vdw 2.294 2.440 ... (remaining 87265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.040 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.870 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 11170 Z= 0.385 Angle : 0.782 11.105 15152 Z= 0.433 Chirality : 0.052 0.382 1735 Planarity : 0.005 0.052 1882 Dihedral : 13.958 106.886 4202 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: -2.62 (0.20), residues: 1341 helix: -1.32 (0.17), residues: 707 sheet: -1.48 (0.33), residues: 216 loop : -2.27 (0.25), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 708 HIS 0.007 0.001 HIS B 355 PHE 0.023 0.002 PHE A 375 TYR 0.016 0.002 TYR B 697 ARG 0.009 0.001 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8234 (tt0) cc_final: 0.7639 (tm-30) REVERT: B 214 ASP cc_start: 0.7127 (t70) cc_final: 0.6714 (t70) REVERT: B 504 ILE cc_start: 0.8550 (tt) cc_final: 0.8320 (tt) REVERT: B 676 TRP cc_start: 0.7708 (t60) cc_final: 0.7303 (t60) outliers start: 0 outliers final: 1 residues processed: 214 average time/residue: 0.9873 time to fit residues: 231.5648 Evaluate side-chains 137 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11170 Z= 0.368 Angle : 0.686 8.727 15152 Z= 0.354 Chirality : 0.048 0.367 1735 Planarity : 0.005 0.067 1882 Dihedral : 8.217 85.198 1660 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.41 % Allowed : 14.32 % Favored : 81.27 % 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: -1.59 (0.21), residues: 1341 helix: -0.38 (0.18), residues: 707 sheet: -1.30 (0.33), residues: 222 loop : -1.84 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 656 HIS 0.007 0.002 HIS A 760 PHE 0.023 0.002 PHE A 375 TYR 0.013 0.002 TYR B 314 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 1.345 Fit side-chains REVERT: A 357 GLN cc_start: 0.8255 (tt0) cc_final: 0.7649 (tm-30) REVERT: B 494 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7456 (tp) REVERT: B 504 ILE cc_start: 0.8537 (tt) cc_final: 0.8314 (tt) REVERT: B 656 TRP cc_start: 0.7376 (m100) cc_final: 0.6281 (m-10) REVERT: B 676 TRP cc_start: 0.7742 (t60) cc_final: 0.7367 (t60) outliers start: 52 outliers final: 25 residues processed: 177 average time/residue: 0.9612 time to fit residues: 186.3630 Evaluate side-chains 160 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 503 ASN B 521 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11170 Z= 0.220 Angle : 0.626 9.723 15152 Z= 0.317 Chirality : 0.044 0.353 1735 Planarity : 0.005 0.049 1882 Dihedral : 6.896 66.842 1660 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.81 % Allowed : 17.80 % Favored : 78.39 % 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: -0.97 (0.22), residues: 1341 helix: 0.16 (0.19), residues: 706 sheet: -0.95 (0.35), residues: 212 loop : -1.69 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 PHE 0.018 0.001 PHE A 375 TYR 0.014 0.001 TYR B 123 ARG 0.005 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8300 (tt0) cc_final: 0.7646 (tm-30) REVERT: A 610 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 757 GLN cc_start: 0.7345 (mt0) cc_final: 0.7037 (mt0) REVERT: A 807 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6133 (ttp) REVERT: A 863 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7273 (tmm160) REVERT: B 206 GLN cc_start: 0.7344 (tp40) cc_final: 0.6782 (tp40) REVERT: B 504 ILE cc_start: 0.8550 (tt) cc_final: 0.8317 (tt) REVERT: B 676 TRP cc_start: 0.7697 (t60) cc_final: 0.7327 (t60) outliers start: 45 outliers final: 23 residues processed: 172 average time/residue: 0.8234 time to fit residues: 156.2792 Evaluate side-chains 162 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11170 Z= 0.226 Angle : 0.624 9.192 15152 Z= 0.313 Chirality : 0.044 0.345 1735 Planarity : 0.004 0.046 1882 Dihedral : 5.902 46.700 1660 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.15 % Allowed : 19.24 % Favored : 76.61 % 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: -0.71 (0.23), residues: 1341 helix: 0.44 (0.19), residues: 707 sheet: -0.80 (0.36), residues: 204 loop : -1.71 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 PHE 0.026 0.002 PHE A 339 TYR 0.018 0.001 TYR B 220 ARG 0.003 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8587 (mmt-90) REVERT: A 357 GLN cc_start: 0.8321 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 610 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 758 LEU cc_start: 0.7471 (mm) cc_final: 0.7142 (mm) REVERT: B 214 ASP cc_start: 0.7102 (t70) cc_final: 0.6709 (t70) REVERT: B 494 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7272 (tp) REVERT: B 504 ILE cc_start: 0.8557 (tt) cc_final: 0.8311 (tt) REVERT: B 676 TRP cc_start: 0.7674 (t60) cc_final: 0.7299 (t60) outliers start: 49 outliers final: 25 residues processed: 179 average time/residue: 0.9437 time to fit residues: 187.4096 Evaluate side-chains 166 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11170 Z= 0.304 Angle : 0.641 9.432 15152 Z= 0.323 Chirality : 0.046 0.339 1735 Planarity : 0.004 0.045 1882 Dihedral : 5.420 40.384 1658 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.00 % Allowed : 20.34 % Favored : 74.66 % 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: -0.70 (0.23), residues: 1341 helix: 0.47 (0.19), residues: 711 sheet: -0.89 (0.35), residues: 208 loop : -1.72 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 708 HIS 0.006 0.001 HIS B 355 PHE 0.021 0.002 PHE A 375 TYR 0.013 0.002 TYR A 678 ARG 0.004 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 141 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8633 (mmt-90) REVERT: A 357 GLN cc_start: 0.8322 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 576 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6798 (p0) REVERT: A 610 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 758 LEU cc_start: 0.7436 (mm) cc_final: 0.7064 (mm) REVERT: B 214 ASP cc_start: 0.7132 (t70) cc_final: 0.6726 (t70) REVERT: B 414 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: B 494 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7277 (tp) REVERT: B 504 ILE cc_start: 0.8547 (tt) cc_final: 0.8315 (tt) REVERT: B 676 TRP cc_start: 0.7688 (t60) cc_final: 0.7332 (t60) outliers start: 59 outliers final: 35 residues processed: 177 average time/residue: 0.8969 time to fit residues: 175.5314 Evaluate side-chains 178 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11170 Z= 0.223 Angle : 0.621 9.611 15152 Z= 0.311 Chirality : 0.044 0.339 1735 Planarity : 0.004 0.044 1882 Dihedral : 5.151 37.569 1658 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.34 % Allowed : 20.08 % Favored : 74.58 % 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: -0.48 (0.23), residues: 1341 helix: 0.67 (0.20), residues: 709 sheet: -0.79 (0.36), residues: 208 loop : -1.66 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 PHE 0.022 0.001 PHE A 339 TYR 0.020 0.001 TYR B 220 ARG 0.005 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 144 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8603 (mmt-90) REVERT: A 357 GLN cc_start: 0.8289 (tt0) cc_final: 0.7593 (tm-30) REVERT: A 576 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6825 (p0) REVERT: A 610 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 214 ASP cc_start: 0.7116 (t70) cc_final: 0.6676 (t70) REVERT: B 414 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: B 494 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7292 (tp) REVERT: B 504 ILE cc_start: 0.8574 (tt) cc_final: 0.8327 (tt) REVERT: B 645 LEU cc_start: 0.6965 (tp) cc_final: 0.6030 (mp) REVERT: B 676 TRP cc_start: 0.7634 (t60) cc_final: 0.7289 (t60) outliers start: 63 outliers final: 35 residues processed: 186 average time/residue: 0.7306 time to fit residues: 150.8114 Evaluate side-chains 180 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 746 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11170 Z= 0.249 Angle : 0.640 9.847 15152 Z= 0.321 Chirality : 0.044 0.338 1735 Planarity : 0.004 0.051 1882 Dihedral : 5.037 35.073 1658 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.92 % Allowed : 21.10 % Favored : 73.98 % 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: -0.40 (0.23), residues: 1341 helix: 0.72 (0.20), residues: 708 sheet: -0.76 (0.36), residues: 209 loop : -1.57 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.019 0.001 PHE A 375 TYR 0.013 0.001 TYR A 678 ARG 0.012 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 143 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8608 (mmt-90) REVERT: A 576 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6845 (p0) REVERT: A 610 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8198 (tt) REVERT: B 214 ASP cc_start: 0.7114 (t70) cc_final: 0.6668 (t70) REVERT: B 414 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 494 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7322 (tp) REVERT: B 504 ILE cc_start: 0.8583 (tt) cc_final: 0.8330 (tt) REVERT: B 676 TRP cc_start: 0.7624 (t60) cc_final: 0.7291 (t60) outliers start: 58 outliers final: 39 residues processed: 182 average time/residue: 0.7596 time to fit residues: 153.0922 Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 584 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 746 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11170 Z= 0.236 Angle : 0.659 10.941 15152 Z= 0.325 Chirality : 0.044 0.339 1735 Planarity : 0.004 0.045 1882 Dihedral : 4.924 32.789 1658 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.66 % Allowed : 22.29 % Favored : 73.05 % 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 (0.23), residues: 1341 helix: 0.82 (0.20), residues: 702 sheet: -0.70 (0.36), residues: 221 loop : -1.53 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.018 0.001 PHE A 645 TYR 0.023 0.002 TYR B 220 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8593 (mmt-90) REVERT: A 340 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6742 (tpp80) REVERT: A 576 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6860 (p0) REVERT: A 610 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 214 ASP cc_start: 0.7113 (t70) cc_final: 0.6704 (t70) REVERT: B 414 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: B 494 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 504 ILE cc_start: 0.8595 (tt) cc_final: 0.8341 (tt) REVERT: B 645 LEU cc_start: 0.6935 (tp) cc_final: 0.5920 (mp) REVERT: B 676 TRP cc_start: 0.7624 (t60) cc_final: 0.7290 (t60) outliers start: 55 outliers final: 37 residues processed: 179 average time/residue: 0.7316 time to fit residues: 145.7068 Evaluate side-chains 185 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 857 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 746 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 124 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11170 Z= 0.208 Angle : 0.654 11.027 15152 Z= 0.322 Chirality : 0.043 0.339 1735 Planarity : 0.004 0.043 1882 Dihedral : 4.786 30.733 1658 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.81 % Allowed : 23.56 % Favored : 72.63 % 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: -0.21 (0.23), residues: 1341 helix: 0.83 (0.20), residues: 710 sheet: -0.54 (0.37), residues: 210 loop : -1.49 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 769 HIS 0.004 0.001 HIS B 355 PHE 0.019 0.001 PHE A 645 TYR 0.013 0.001 TYR A 678 ARG 0.011 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8562 (mmt-90) REVERT: A 340 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6732 (tpp80) REVERT: A 576 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6872 (p0) REVERT: A 610 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 214 ASP cc_start: 0.7092 (t70) cc_final: 0.6687 (t70) REVERT: B 494 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7283 (tp) REVERT: B 504 ILE cc_start: 0.8594 (tt) cc_final: 0.8339 (tt) REVERT: B 645 LEU cc_start: 0.6881 (tp) cc_final: 0.6291 (mm) REVERT: B 676 TRP cc_start: 0.7594 (t60) cc_final: 0.7265 (t60) outliers start: 45 outliers final: 33 residues processed: 171 average time/residue: 0.6300 time to fit residues: 119.9213 Evaluate side-chains 178 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 746 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 0.0070 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: