Starting phenix.real_space_refine on Wed Mar 4 20:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430.map" model { file = "/net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stj_25430/03_2026/7stj_25430_neut.cif" } resolution = 4.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3406 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8597 2.51 5 N 2320 2.21 5 O 2490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6378 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 743} Chain breaks: 9 Chain: "B" Number of atoms: 6441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6441 Classifications: {'peptide': 797} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 752} Chain breaks: 6 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain breaks: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.24 Number of scatterers: 13515 At special positions: 0 Unit cell: (131.76, 132.84, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2490 8.00 N 2320 7.00 C 8597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.02 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.02 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.04 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 449.4 milliseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.877A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.742A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.537A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.734A pdb=" N LEU A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 869 Processing helix chain 'B' and resid 17 through 25 removed outlier: 4.012A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN B 25 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.370A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.531A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 323 through 329 removed outlier: 4.238A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.168A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.156A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.767A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 705 through 714 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.657A pdb=" N ASP B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 870 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.665A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.872A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.568A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.023A pdb=" N LEU A 33 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET A 98 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET A 98 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 311 removed outlier: 6.199A pdb=" N LYS A 310 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 336 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 363 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.740A pdb=" N LYS A 319 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 341 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 473 Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 479 Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.638A pdb=" N MET A 504 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 567 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 598 through 604 removed outlier: 5.314A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.860A pdb=" N GLY A 778 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB5, first strand: chain 'A' and resid 857 through 862 removed outlier: 3.620A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL A 886 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP A 897 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA A 888 " --> pdb=" O GLY A 895 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 880 through 881 Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13 removed outlier: 8.832A pdb=" N GLN B 34 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET B 98 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ARG B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC2, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.501A pdb=" N THR B 293 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.160A pdb=" N VAL B 335 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN B 313 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 337 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 315 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 339 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY B 317 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 341 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 364 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.160A pdb=" N VAL B 335 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN B 313 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 337 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 315 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 339 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY B 317 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 341 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.906A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 599 through 605 removed outlier: 4.567A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 762 Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.583A pdb=" N ALA B 803 " --> pdb=" O TYR B 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 818 through 822 removed outlier: 3.563A pdb=" N CYS B 872 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 856 through 862 334 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.76 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: 4409 1.34 - 1.46: 3296 1.46 - 1.58: 6007 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 13844 Sorted by residual: bond pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " ideal model delta sigma weight residual 1.539 1.455 0.084 4.88e-02 4.20e+02 2.98e+00 bond pdb=" C LYS B 197 " pdb=" N SER B 198 " ideal model delta sigma weight residual 1.332 1.310 0.023 1.40e-02 5.10e+03 2.66e+00 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.528 1.513 0.016 1.04e-02 9.25e+03 2.30e+00 bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.519 1.501 0.018 1.22e-02 6.72e+03 2.18e+00 bond pdb=" CA CYS A 308 " pdb=" C CYS A 308 " ideal model delta sigma weight residual 1.531 1.521 0.011 7.40e-03 1.83e+04 2.02e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18445 2.36 - 4.71: 281 4.71 - 7.07: 26 7.07 - 9.43: 2 9.43 - 11.79: 2 Bond angle restraints: 18756 Sorted by residual: angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 113.55 101.76 11.79 1.26e+00 6.30e-01 8.75e+01 angle pdb=" N LEU A 305 " pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 113.20 108.47 4.73 1.21e+00 6.83e-01 1.53e+01 angle pdb=" CB MET A 442 " pdb=" CG MET A 442 " pdb=" SD MET A 442 " ideal model delta sigma weight residual 112.70 123.84 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA TRP B 414 " pdb=" CB TRP B 414 " pdb=" CG TRP B 414 " ideal model delta sigma weight residual 113.60 107.46 6.14 1.90e+00 2.77e-01 1.04e+01 angle pdb=" N ASN A 470 " pdb=" CA ASN A 470 " pdb=" C ASN A 470 " ideal model delta sigma weight residual 110.80 117.39 -6.59 2.13e+00 2.20e-01 9.58e+00 ... (remaining 18751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7507 17.94 - 35.89: 738 35.89 - 53.83: 106 53.83 - 71.78: 19 71.78 - 89.72: 11 Dihedral angle restraints: 8381 sinusoidal: 3498 harmonic: 4883 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.28 -89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -167.36 81.36 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual -86.00 -166.25 80.25 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 8378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1301 0.034 - 0.069: 466 0.069 - 0.103: 193 0.103 - 0.138: 64 0.138 - 0.172: 11 Chirality restraints: 2035 Sorted by residual: chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA MET A 442 " pdb=" N MET A 442 " pdb=" C MET A 442 " pdb=" CB MET A 442 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 2032 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 469 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C GLU B 469 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 469 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 470 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 834 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 835 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 835 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 835 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " -0.013 2.00e-02 2.50e+03 9.67e-03 2.34e+00 pdb=" CG TRP B 414 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.003 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 357 2.62 - 3.19: 13749 3.19 - 3.76: 24225 3.76 - 4.33: 33478 4.33 - 4.90: 50161 Nonbonded interactions: 121970 Sorted by model distance: nonbonded pdb=" O LEU B 552 " pdb=" NH1 ARG B 554 " model vdw 2.047 3.120 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASP B 812 " pdb=" OG SER B 890 " model vdw 2.081 3.040 nonbonded pdb=" O HIS A 263 " pdb=" NE2 GLN A 276 " model vdw 2.105 3.120 nonbonded pdb=" O GLU C 59 " pdb=" OG1 THR C 63 " model vdw 2.117 3.040 ... (remaining 121965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 526 or resid 529 through 656 or resid 704 throug \ h 905)) selection = (chain 'B' and (resid 3 through 150 or resid 168 through 172 or resid 178 throug \ h 314 or resid 317 through 346 or resid 351 through 539 or resid 547 through 905 \ )) } ncs_group { reference = (chain 'C' and (resid 7 through 26 or resid 56 through 76)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.005 0.084 13881 Z= 0.254 Angle : 0.718 11.787 18830 Z= 0.384 Chirality : 0.045 0.172 2035 Planarity : 0.005 0.048 2416 Dihedral : 13.424 86.749 5114 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 36.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.00 % Favored : 89.88 % Rotamer: Outliers : 0.33 % Allowed : 0.59 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1630 helix: -1.37 (0.36), residues: 187 sheet: -1.39 (0.27), residues: 354 loop : -1.28 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 65 TYR 0.021 0.002 TYR A 277 PHE 0.016 0.002 PHE B 565 TRP 0.024 0.002 TRP B 414 HIS 0.006 0.002 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00540 (13844) covalent geometry : angle 0.71574 (18756) SS BOND : bond 0.00336 ( 37) SS BOND : angle 1.18541 ( 74) hydrogen bonds : bond 0.31546 ( 322) hydrogen bonds : angle 9.88635 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: B 38 MET cc_start: 0.7913 (mmp) cc_final: 0.7605 (mmp) REVERT: B 553 MET cc_start: 0.9239 (mmp) cc_final: 0.8927 (mmm) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.0995 time to fit residues: 7.3976 Evaluate side-chains 38 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 21 HIS ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS B 275 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.035028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.023403 restraints weight = 220970.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.024043 restraints weight = 127009.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.024478 restraints weight = 89441.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.024688 restraints weight = 71879.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.024875 restraints weight = 63251.825| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 13881 Z= 0.307 Angle : 0.753 8.120 18830 Z= 0.394 Chirality : 0.046 0.157 2035 Planarity : 0.005 0.052 2416 Dihedral : 5.412 24.204 1824 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.07 % Allowed : 7.88 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.20), residues: 1630 helix: -1.79 (0.31), residues: 219 sheet: -1.52 (0.28), residues: 337 loop : -1.43 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 554 TYR 0.022 0.002 TYR A 430 PHE 0.014 0.002 PHE A 400 TRP 0.020 0.002 TRP B 414 HIS 0.009 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00656 (13844) covalent geometry : angle 0.75069 (18756) SS BOND : bond 0.00388 ( 37) SS BOND : angle 1.14236 ( 74) hydrogen bonds : bond 0.06061 ( 322) hydrogen bonds : angle 8.28251 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8802 (tpt) cc_final: 0.8543 (tpp) REVERT: A 300 MET cc_start: 0.9762 (tpt) cc_final: 0.9500 (tpt) REVERT: A 831 MET cc_start: 0.8569 (tpt) cc_final: 0.8124 (tpt) REVERT: B 98 MET cc_start: 0.7863 (mmp) cc_final: 0.7374 (mmm) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0902 time to fit residues: 5.9018 Evaluate side-chains 33 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 34 GLN A 276 GLN A 295 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 187 HIS B 431 ASN D 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.035763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.024066 restraints weight = 219653.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.024808 restraints weight = 121750.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.025248 restraints weight = 83381.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.025499 restraints weight = 65774.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.025630 restraints weight = 57172.649| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13881 Z= 0.167 Angle : 0.613 6.190 18830 Z= 0.323 Chirality : 0.045 0.154 2035 Planarity : 0.004 0.047 2416 Dihedral : 5.113 20.940 1824 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.21), residues: 1630 helix: -1.41 (0.33), residues: 219 sheet: -1.46 (0.29), residues: 334 loop : -1.42 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 554 TYR 0.016 0.001 TYR B 845 PHE 0.024 0.002 PHE A 248 TRP 0.022 0.002 TRP B 414 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00368 (13844) covalent geometry : angle 0.61119 (18756) SS BOND : bond 0.00291 ( 37) SS BOND : angle 0.92858 ( 74) hydrogen bonds : bond 0.04832 ( 322) hydrogen bonds : angle 7.67360 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8653 (tpt) cc_final: 0.8400 (tpp) REVERT: A 300 MET cc_start: 0.9791 (tpt) cc_final: 0.9561 (tpt) REVERT: A 831 MET cc_start: 0.8744 (tpt) cc_final: 0.8327 (tpt) REVERT: B 98 MET cc_start: 0.7614 (mmp) cc_final: 0.7252 (mmm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0905 time to fit residues: 6.5600 Evaluate side-chains 33 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.036015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.024516 restraints weight = 215161.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.024871 restraints weight = 145114.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.025279 restraints weight = 92174.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.025246 restraints weight = 82300.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.025273 restraints weight = 71971.811| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13881 Z= 0.135 Angle : 0.584 8.154 18830 Z= 0.305 Chirality : 0.044 0.159 2035 Planarity : 0.004 0.046 2416 Dihedral : 4.929 20.295 1824 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.21), residues: 1630 helix: -1.17 (0.34), residues: 219 sheet: -1.41 (0.28), residues: 338 loop : -1.35 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.015 0.001 TYR C 16 PHE 0.019 0.001 PHE A 565 TRP 0.023 0.001 TRP B 414 HIS 0.004 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00305 (13844) covalent geometry : angle 0.58351 (18756) SS BOND : bond 0.00428 ( 37) SS BOND : angle 0.79632 ( 74) hydrogen bonds : bond 0.04112 ( 322) hydrogen bonds : angle 7.16737 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7288 (tpt) cc_final: 0.7033 (mmm) REVERT: A 300 MET cc_start: 0.9819 (tpt) cc_final: 0.9577 (tpt) REVERT: A 831 MET cc_start: 0.8765 (tpt) cc_final: 0.8331 (tpt) REVERT: B 553 MET cc_start: 0.9264 (mmm) cc_final: 0.8976 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0907 time to fit residues: 6.3200 Evaluate side-chains 32 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 40.0000 chunk 44 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.035040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.024135 restraints weight = 223786.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.024352 restraints weight = 149593.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.024282 restraints weight = 105492.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.024366 restraints weight = 100511.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.024423 restraints weight = 89300.557| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 13881 Z= 0.264 Angle : 0.681 7.110 18830 Z= 0.353 Chirality : 0.045 0.217 2035 Planarity : 0.005 0.065 2416 Dihedral : 5.196 23.033 1824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1630 helix: -1.44 (0.33), residues: 219 sheet: -1.55 (0.29), residues: 322 loop : -1.37 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 780 TYR 0.020 0.002 TYR B 562 PHE 0.015 0.002 PHE B 76 TRP 0.024 0.002 TRP B 414 HIS 0.009 0.002 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00571 (13844) covalent geometry : angle 0.67822 (18756) SS BOND : bond 0.00446 ( 37) SS BOND : angle 1.16005 ( 74) hydrogen bonds : bond 0.04406 ( 322) hydrogen bonds : angle 7.39215 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7490 (tpt) cc_final: 0.7046 (mmm) REVERT: A 831 MET cc_start: 0.8713 (tpt) cc_final: 0.8237 (tpt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0941 time to fit residues: 6.2267 Evaluate side-chains 33 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 38 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.035611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.023766 restraints weight = 217490.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.024531 restraints weight = 118009.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.024997 restraints weight = 79822.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.025248 restraints weight = 62303.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.025384 restraints weight = 53537.826| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13881 Z= 0.152 Angle : 0.601 7.576 18830 Z= 0.310 Chirality : 0.045 0.211 2035 Planarity : 0.004 0.046 2416 Dihedral : 5.031 21.273 1824 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.21), residues: 1630 helix: -1.16 (0.34), residues: 219 sheet: -1.39 (0.29), residues: 318 loop : -1.39 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.018 0.001 TYR B 562 PHE 0.012 0.001 PHE A 565 TRP 0.020 0.002 TRP B 414 HIS 0.005 0.001 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00343 (13844) covalent geometry : angle 0.59887 (18756) SS BOND : bond 0.00298 ( 37) SS BOND : angle 0.96406 ( 74) hydrogen bonds : bond 0.03873 ( 322) hydrogen bonds : angle 7.05667 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8647 (tpt) cc_final: 0.8196 (tpt) REVERT: B 98 MET cc_start: 0.7816 (mmp) cc_final: 0.7565 (mmm) REVERT: B 806 MET cc_start: 0.9360 (mpp) cc_final: 0.9157 (mpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1021 time to fit residues: 6.9821 Evaluate side-chains 35 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 0.2980 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 152 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 148 ASN A 405 ASN A 431 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.036410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.024567 restraints weight = 209504.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.025327 restraints weight = 118753.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.025800 restraints weight = 80475.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.026094 restraints weight = 62377.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.026198 restraints weight = 53415.684| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13881 Z= 0.104 Angle : 0.602 9.253 18830 Z= 0.306 Chirality : 0.045 0.189 2035 Planarity : 0.004 0.047 2416 Dihedral : 4.740 18.060 1824 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.21), residues: 1630 helix: -1.00 (0.34), residues: 220 sheet: -1.16 (0.29), residues: 314 loop : -1.38 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 86 TYR 0.017 0.001 TYR B 562 PHE 0.014 0.001 PHE A 565 TRP 0.018 0.001 TRP B 414 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00235 (13844) covalent geometry : angle 0.60068 (18756) SS BOND : bond 0.00249 ( 37) SS BOND : angle 0.88897 ( 74) hydrogen bonds : bond 0.03597 ( 322) hydrogen bonds : angle 6.58097 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8783 (tpt) cc_final: 0.8367 (tpt) REVERT: B 23 LEU cc_start: 0.9389 (mt) cc_final: 0.9041 (tt) REVERT: B 553 MET cc_start: 0.9461 (mmm) cc_final: 0.9189 (mmm) REVERT: B 806 MET cc_start: 0.9363 (mpp) cc_final: 0.9162 (mpp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0900 time to fit residues: 6.7961 Evaluate side-chains 36 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 153 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 431 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.035926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.024584 restraints weight = 214819.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.025079 restraints weight = 142870.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.025485 restraints weight = 88761.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.025429 restraints weight = 80893.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.025461 restraints weight = 74161.106| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13881 Z= 0.130 Angle : 0.581 7.773 18830 Z= 0.300 Chirality : 0.044 0.174 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.719 18.860 1824 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.21), residues: 1630 helix: -1.03 (0.35), residues: 220 sheet: -1.16 (0.29), residues: 323 loop : -1.40 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 47 TYR 0.019 0.001 TYR B 562 PHE 0.010 0.001 PHE A 565 TRP 0.020 0.001 TRP B 414 HIS 0.005 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00295 (13844) covalent geometry : angle 0.57643 (18756) SS BOND : bond 0.00233 ( 37) SS BOND : angle 1.34204 ( 74) hydrogen bonds : bond 0.03642 ( 322) hydrogen bonds : angle 6.58260 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8714 (tpt) cc_final: 0.8268 (tpt) REVERT: B 98 MET cc_start: 0.7726 (mmp) cc_final: 0.7517 (mmm) REVERT: B 507 TYR cc_start: 0.8302 (p90) cc_final: 0.8097 (p90) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0756 time to fit residues: 5.6230 Evaluate side-chains 35 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 160 optimal weight: 0.0970 chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.035444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.023746 restraints weight = 220217.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.024528 restraints weight = 118108.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.024983 restraints weight = 79249.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.025265 restraints weight = 61600.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.025404 restraints weight = 52732.709| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13881 Z= 0.173 Angle : 0.611 9.561 18830 Z= 0.314 Chirality : 0.044 0.217 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.842 20.985 1824 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.21), residues: 1630 helix: -1.08 (0.35), residues: 213 sheet: -1.14 (0.29), residues: 322 loop : -1.33 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 850 TYR 0.018 0.001 TYR B 562 PHE 0.012 0.001 PHE A 565 TRP 0.023 0.002 TRP B 632 HIS 0.005 0.001 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00382 (13844) covalent geometry : angle 0.60857 (18756) SS BOND : bond 0.00242 ( 37) SS BOND : angle 1.11349 ( 74) hydrogen bonds : bond 0.03719 ( 322) hydrogen bonds : angle 6.61831 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8722 (tpt) cc_final: 0.8250 (tpt) REVERT: B 98 MET cc_start: 0.7595 (mmp) cc_final: 0.7391 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0938 time to fit residues: 6.5807 Evaluate side-chains 33 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 96 optimal weight: 0.0270 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.035537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023998 restraints weight = 216841.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.024731 restraints weight = 122033.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.025164 restraints weight = 83735.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.025410 restraints weight = 66123.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.025492 restraints weight = 57266.211| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13881 Z= 0.138 Angle : 0.591 10.502 18830 Z= 0.303 Chirality : 0.044 0.175 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.792 19.479 1824 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.21), residues: 1630 helix: -1.04 (0.35), residues: 214 sheet: -1.14 (0.29), residues: 324 loop : -1.32 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 850 TYR 0.027 0.001 TYR B 562 PHE 0.009 0.001 PHE A 248 TRP 0.021 0.001 TRP B 414 HIS 0.004 0.001 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00311 (13844) covalent geometry : angle 0.58853 (18756) SS BOND : bond 0.00234 ( 37) SS BOND : angle 1.02010 ( 74) hydrogen bonds : bond 0.03546 ( 322) hydrogen bonds : angle 6.50588 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.8763 (tpt) cc_final: 0.8313 (tpt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0897 time to fit residues: 5.9881 Evaluate side-chains 34 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 60 optimal weight: 50.0000 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.035182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.023718 restraints weight = 218961.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.024409 restraints weight = 123534.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.024859 restraints weight = 85683.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.025111 restraints weight = 67297.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.025181 restraints weight = 58246.512| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13881 Z= 0.176 Angle : 0.612 9.724 18830 Z= 0.313 Chirality : 0.044 0.191 2035 Planarity : 0.004 0.045 2416 Dihedral : 4.889 20.945 1824 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.21), residues: 1630 helix: -1.04 (0.35), residues: 214 sheet: -1.22 (0.29), residues: 330 loop : -1.30 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 47 TYR 0.021 0.001 TYR B 562 PHE 0.012 0.001 PHE A 400 TRP 0.022 0.002 TRP B 414 HIS 0.005 0.001 HIS B 627 Details of bonding type rmsd covalent geometry : bond 0.00391 (13844) covalent geometry : angle 0.60939 (18756) SS BOND : bond 0.00258 ( 37) SS BOND : angle 1.03997 ( 74) hydrogen bonds : bond 0.03663 ( 322) hydrogen bonds : angle 6.61553 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.76 seconds wall clock time: 45 minutes 41.89 seconds (2741.89 seconds total)