Starting phenix.real_space_refine (version: dev) on Sun Feb 19 23:41:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/02_2023/7c7s_30301_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 chiralities: 3 Time building chain proxies: 6.47, per 1000 atoms: 0.59 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: 3.99 Conformation dependent library (CDL) restraints added in 1.5 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: 1.29 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: 3.25 Time building geometry restraints manager: 4.37 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 1.386 1.486 -0.100 2.00e-02 2.50e+03 2.49e+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=" C GLU B 649 " pdb=" N ASN B 650 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.40e-02 5.10e+03 5.89e+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=" C2 2BV A1006 " pdb=" N 2BV A1006 " pdb=" C9 2BV A1006 " ideal model delta sigma weight residual 109.47 123.47 -14.00 3.00e+00 1.11e-01 2.18e+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 ... (remaining 15147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 6381 27.69 - 55.38: 215 55.38 - 83.07: 17 83.07 - 110.75: 3 110.75 - 138.44: 1 Dihedral angle restraints: 6617 sinusoidal: 2680 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 6614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.047: 1734 1.047 - 2.094: 0 2.094 - 3.141: 0 3.141 - 4.188: 0 4.188 - 5.235: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C13 2BV A1006 " pdb=" C12 2BV A1006 " pdb=" C14 2BV A1006 " pdb=" C18 2BV A1006 " both_signs ideal model delta sigma weight residual False -2.73 2.50 -5.24 2.00e-01 2.50e+01 6.85e+02 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 -2.60 -2.13 -0.48 2.00e-01 2.50e+01 5.68e+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 ... (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 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. 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.610 Check model and map are aligned: 0.170 Process input model: 29.310 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.100 11170 Z= 0.378 Angle : 0.767 14.002 15152 Z= 0.430 Chirality : 0.136 5.235 1735 Planarity : 0.005 0.052 1882 Dihedral : 13.592 138.442 4062 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 % 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 *********************** 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 : 1.415 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 214 average time/residue: 1.0669 time to fit residues: 249.8887 Evaluate side-chains 137 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 11170 Z= 0.372 Angle : 0.687 9.056 15152 Z= 0.356 Chirality : 0.048 0.363 1735 Planarity : 0.005 0.068 1882 Dihedral : 7.121 117.230 1518 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 4.15 % 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: -1.61 (0.21), residues: 1341 helix: -0.41 (0.18), residues: 705 sheet: -1.27 (0.33), residues: 220 loop : -1.85 (0.28), residues: 416 *********************** 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 199 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.369 Fit side-chains outliers start: 49 outliers final: 26 residues processed: 175 average time/residue: 1.0349 time to fit residues: 199.2301 Evaluate side-chains 157 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 14 residues processed: 12 average time/residue: 0.1836 time to fit residues: 4.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11170 Z= 0.199 Angle : 0.616 8.785 15152 Z= 0.312 Chirality : 0.044 0.349 1735 Planarity : 0.005 0.048 1882 Dihedral : 6.838 108.416 1518 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 3.64 % 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: -0.94 (0.22), residues: 1341 helix: 0.20 (0.19), residues: 706 sheet: -0.91 (0.35), residues: 211 loop : -1.69 (0.28), residues: 424 *********************** 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 190 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.474 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 177 average time/residue: 0.9264 time to fit residues: 181.4986 Evaluate side-chains 155 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.2881 time to fit residues: 4.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN ** B 126 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: 0.8032 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11170 Z= 0.221 Angle : 0.613 9.474 15152 Z= 0.310 Chirality : 0.044 0.319 1735 Planarity : 0.004 0.046 1882 Dihedral : 6.766 107.222 1518 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 4.41 % 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: -0.63 (0.23), residues: 1341 helix: 0.48 (0.20), residues: 705 sheet: -0.77 (0.36), residues: 212 loop : -1.62 (0.29), residues: 424 *********************** 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 195 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 143 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 26 residues processed: 179 average time/residue: 0.9404 time to fit residues: 186.2418 Evaluate side-chains 163 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.2844 time to fit residues: 4.4752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 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: 0.9982 ------------------------------------------------------------------------------- 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 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11170 Z= 0.269 Angle : 0.629 9.430 15152 Z= 0.316 Chirality : 0.045 0.321 1735 Planarity : 0.004 0.045 1882 Dihedral : 6.766 106.337 1518 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 4.66 % 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: -0.57 (0.23), residues: 1341 helix: 0.56 (0.20), residues: 708 sheet: -0.84 (0.35), residues: 221 loop : -1.63 (0.29), residues: 412 *********************** 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: 55 poor density : 145 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 179 average time/residue: 0.9366 time to fit residues: 185.8594 Evaluate side-chains 164 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 20 residues processed: 10 average time/residue: 0.2688 time to fit residues: 5.3886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 108 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 407 ASN B 414 GLN B 595 GLN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2299 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= 0.216 Angle : 0.614 9.689 15152 Z= 0.307 Chirality : 0.044 0.321 1735 Planarity : 0.004 0.044 1882 Dihedral : 6.700 106.596 1518 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 4.58 % 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: -0.39 (0.23), residues: 1341 helix: 0.75 (0.20), residues: 703 sheet: -0.75 (0.36), residues: 209 loop : -1.59 (0.28), residues: 429 *********************** 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 191 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 30 residues processed: 177 average time/residue: 0.9147 time to fit residues: 179.8671 Evaluate side-chains 163 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 7 average time/residue: 0.1774 time to fit residues: 3.6425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 407 ASN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11170 Z= 0.249 Angle : 0.655 9.971 15152 Z= 0.324 Chirality : 0.045 0.319 1735 Planarity : 0.004 0.043 1882 Dihedral : 6.713 106.222 1518 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.98 % 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: -0.35 (0.23), residues: 1341 helix: 0.74 (0.20), residues: 708 sheet: -0.76 (0.36), residues: 220 loop : -1.52 (0.29), residues: 413 *********************** 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 187 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.629 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 169 average time/residue: 0.9033 time to fit residues: 169.8593 Evaluate side-chains 168 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 9 average time/residue: 0.2527 time to fit residues: 4.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 595 GLN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11170 Z= 0.258 Angle : 0.664 10.631 15152 Z= 0.328 Chirality : 0.045 0.320 1735 Planarity : 0.005 0.069 1882 Dihedral : 6.722 106.285 1518 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.64 % 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: -0.33 (0.23), residues: 1341 helix: 0.78 (0.20), residues: 703 sheet: -0.76 (0.36), residues: 220 loop : -1.51 (0.29), residues: 418 *********************** 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 190 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.321 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 32 residues processed: 177 average time/residue: 0.8959 time to fit residues: 176.6279 Evaluate side-chains 169 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 9 average time/residue: 0.1856 time to fit residues: 4.1976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11170 Z= 0.270 Angle : 0.666 10.764 15152 Z= 0.331 Chirality : 0.045 0.320 1735 Planarity : 0.005 0.060 1882 Dihedral : 6.749 106.323 1518 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 3.56 % 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: -0.35 (0.23), residues: 1341 helix: 0.72 (0.20), residues: 709 sheet: -0.77 (0.36), residues: 222 loop : -1.48 (0.29), residues: 410 *********************** 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 179 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.341 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 167 average time/residue: 0.9358 time to fit residues: 174.4615 Evaluate side-chains 164 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 8 average time/residue: 0.3033 time to fit residues: 5.0276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 134 optimal weight: 0.1980 chunk 123 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11170 Z= 0.239 Angle : 0.696 11.840 15152 Z= 0.339 Chirality : 0.045 0.319 1735 Planarity : 0.004 0.058 1882 Dihedral : 6.727 106.887 1518 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.80 % 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: -0.28 (0.23), residues: 1341 helix: 0.81 (0.20), residues: 703 sheet: -0.73 (0.36), residues: 220 loop : -1.49 (0.29), residues: 418 ********************** REFINEMENT MACRO_CYCLE 10 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 173 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 168 average time/residue: 0.9150 time to fit residues: 171.2151 Evaluate side-chains 164 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 0.2293 time to fit residues: 2.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 B 521 ASN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076666 restraints weight = 22636.235| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.12 r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11170 Z= 0.240 Angle : 0.671 10.543 15152 Z= 0.332 Chirality : 0.044 0.316 1735 Planarity : 0.005 0.070 1882 Dihedral : 6.746 106.979 1518 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 2.54 % 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: -0.24 (0.23), residues: 1341 helix: 0.84 (0.20), residues: 703 sheet: -0.74 (0.36), residues: 221 loop : -1.43 (0.30), residues: 417 =============================================================================== Job complete usr+sys time: 3784.82 seconds wall clock time: 68 minutes 37.04 seconds (4117.04 seconds total)