Starting phenix.real_space_refine on Thu Mar 5 07:33:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ui7_26541/03_2026/7ui7_26541.map" } resolution = 3.4 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 S 54 5.16 5 C 6606 2.51 5 N 1746 2.21 5 O 1804 1.98 5 H 10079 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 20293 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 10145 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 23, 'TRANS': 589} Chain breaks: 1 Chain: "B" Number of atoms: 10144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 10144 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 23, 'TRANS': 589} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.12, per 1000 atoms: 0.20 Number of scatterers: 20293 At special positions: 0 Unit cell: (115.416, 106.6, 104.195, 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) Mn 4 24.99 S 54 16.00 O 1804 8.00 N 1746 7.00 C 6606 6.00 H 10079 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 726 " 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: 1.89 Conformation dependent library (CDL) restraints added in 637.5 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 48.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.734A pdb=" N THR A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.764A pdb=" N VAL A 208 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.517A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.008A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.590A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.735A pdb=" N ASN A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.791A pdb=" N CYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.581A pdb=" N VAL A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.864A pdb=" N PHE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.725A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 removed outlier: 5.855A pdb=" N GLN A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.614A pdb=" N HIS A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.617A pdb=" N GLN A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.631A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.847A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.612A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 634 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix No H-bonds generated for 'chain 'A' and resid 630 through 637' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.838A pdb=" N TRP A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.722A pdb=" N GLN A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.723A pdb=" N THR A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 743 removed outlier: 3.909A pdb=" N ARG A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.810A pdb=" N LEU A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.215A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.691A pdb=" N MET B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.563A pdb=" N VAL B 208 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 4.286A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.035A pdb=" N MET B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.522A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.648A pdb=" N ASN B 357 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.934A pdb=" N GLN B 368 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.959A pdb=" N VAL B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.500A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.770A pdb=" N GLU B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.032A pdb=" N ARG B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.163A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.876A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.680A pdb=" N HIS B 634 " --> pdb=" O THR B 631 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.664A pdb=" N TRP B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 680 through 691 removed outlier: 4.147A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.922A pdb=" N THR B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 743 removed outlier: 3.690A pdb=" N ARG B 724 " --> pdb=" O ASN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 removed outlier: 4.119A pdb=" N LEU B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.688A pdb=" N LEU A 168 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP A 197 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 170 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR A 199 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 172 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.593A pdb=" N ILE A 379 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.581A pdb=" N ILE A 533 " --> pdb=" O HIS A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 530 removed outlier: 7.022A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 649 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 599 Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.921A pdb=" N LEU B 168 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASP B 197 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 170 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR B 199 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 172 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 138 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N HIS B 171 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 140 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 173 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 142 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.896A pdb=" N HIS B 380 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 7.365A pdb=" N LEU B 269 " --> pdb=" O LEU B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AB1, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.073A pdb=" N LEU B 480 " --> pdb=" O ALA B 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 558 through 560 removed outlier: 5.103A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA B 591 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 649 " --> pdb=" O VAL B 697 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 933 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: 4.98 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10071 1.03 - 1.23: 32 1.23 - 1.43: 4554 1.43 - 1.62: 5818 1.62 - 1.82: 92 Bond restraints: 20567 Sorted by residual: bond pdb=" C HIS A 705 " pdb=" N MET A 706 " ideal model delta sigma weight residual 1.332 1.359 -0.026 1.44e-02 4.82e+03 3.37e+00 bond pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 bond pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 1.522 1.499 0.022 1.72e-02 3.38e+03 1.68e+00 bond pdb=" CB VAL A 682 " pdb=" CG1 VAL A 682 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CG GLU B 321 " pdb=" CD GLU B 321 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.74e-01 ... (remaining 20562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 36324 1.58 - 3.16: 679 3.16 - 4.74: 59 4.74 - 6.32: 5 6.32 - 7.90: 3 Bond angle restraints: 37070 Sorted by residual: angle pdb=" CA GLN B 691 " pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " pdb=" CD GLN B 691 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" C ALA B 320 " pdb=" N GLU B 321 " pdb=" CA GLU B 321 " ideal model delta sigma weight residual 120.31 115.56 4.75 1.52e+00 4.33e-01 9.78e+00 angle pdb=" N GLU B 321 " pdb=" CA GLU B 321 " pdb=" CB GLU B 321 " ideal model delta sigma weight residual 110.28 114.84 -4.56 1.55e+00 4.16e-01 8.66e+00 angle pdb=" N GLU A 732 " pdb=" CA GLU A 732 " pdb=" CB GLU A 732 " ideal model delta sigma weight residual 110.12 113.98 -3.86 1.47e+00 4.63e-01 6.89e+00 ... (remaining 37065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8640 16.89 - 33.78: 779 33.78 - 50.67: 195 50.67 - 67.57: 58 67.57 - 84.46: 13 Dihedral angle restraints: 9685 sinusoidal: 5126 harmonic: 4559 Sorted by residual: dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 726 " pdb=" CB CYS A 726 " ideal model delta sinusoidal sigma weight residual 93.00 134.40 -41.40 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA MET A 703 " pdb=" C MET A 703 " pdb=" N ILE A 704 " pdb=" CA ILE A 704 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 432 " pdb=" C LYS A 432 " pdb=" N GLN A 433 " pdb=" CA GLN A 433 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1028 0.034 - 0.068: 358 0.068 - 0.102: 93 0.102 - 0.136: 43 0.136 - 0.170: 8 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA ILE A 300 " pdb=" N ILE A 300 " pdb=" C ILE A 300 " pdb=" CB ILE A 300 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA VAL B 662 " pdb=" N VAL B 662 " pdb=" C VAL B 662 " pdb=" CB VAL B 662 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA VAL A 662 " pdb=" N VAL A 662 " pdb=" C VAL A 662 " pdb=" CB VAL A 662 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1527 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 679 " 0.022 2.00e-02 2.50e+03 1.85e-02 1.37e+01 pdb=" CG TRP A 679 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 679 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 679 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 679 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 679 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 679 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 679 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 679 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 679 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 679 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 679 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 679 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 679 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 679 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 679 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 691 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN B 691 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN B 691 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 692 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 567 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO B 568 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 568 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 568 " 0.031 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 840 2.15 - 2.76: 39026 2.76 - 3.37: 57070 3.37 - 3.99: 71257 3.99 - 4.60: 111646 Nonbonded interactions: 279839 Sorted by model distance: nonbonded pdb=" OD1 ASN A 296 " pdb="HD22 ASN A 357 " model vdw 1.533 2.450 nonbonded pdb=" O GLU B 236 " pdb=" H LEU B 304 " model vdw 1.562 2.450 nonbonded pdb="HE22 GLN A 264 " pdb=" O PHE A 347 " model vdw 1.584 2.450 nonbonded pdb=" H ASN B 272 " pdb=" O GLY B 294 " model vdw 1.593 2.450 nonbonded pdb=" O SER B 206 " pdb=" HG SER B 209 " model vdw 1.604 2.450 ... (remaining 279834 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 133 through 379 or (resid 380 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 381 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.940 Find NCS groups from input model: 0.270 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 0.004 0.046 10492 Z= 0.185 Angle : 0.612 7.903 14226 Z= 0.339 Chirality : 0.041 0.170 1530 Planarity : 0.004 0.057 1796 Dihedral : 14.826 84.457 3852 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.83 (0.23), residues: 1218 helix: -0.66 (0.24), residues: 414 sheet: -1.85 (0.41), residues: 138 loop : -1.41 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 740 TYR 0.016 0.002 TYR B 670 PHE 0.019 0.002 PHE B 625 TRP 0.058 0.002 TRP A 679 HIS 0.022 0.001 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00383 (10488) covalent geometry : angle 0.61183 (14218) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.99507 ( 8) hydrogen bonds : bond 0.18339 ( 338) hydrogen bonds : angle 7.11684 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLU cc_start: 0.6792 (tp30) cc_final: 0.6441 (tm-30) REVERT: A 528 ASN cc_start: 0.8026 (p0) cc_final: 0.7763 (p0) REVERT: A 574 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 603 ARG cc_start: 0.7537 (mtt-85) cc_final: 0.7260 (mtt-85) REVERT: B 158 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7167 (tttm) REVERT: B 187 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 197 ASP cc_start: 0.7907 (m-30) cc_final: 0.7619 (m-30) REVERT: B 436 GLU cc_start: 0.7498 (pm20) cc_final: 0.7249 (mp0) REVERT: B 445 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7337 (mp0) REVERT: B 548 ASN cc_start: 0.7910 (p0) cc_final: 0.7599 (p0) REVERT: B 652 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6894 (mm-30) REVERT: B 654 GLU cc_start: 0.7671 (mp0) cc_final: 0.7215 (mp0) REVERT: B 656 ASP cc_start: 0.7405 (m-30) cc_final: 0.7125 (m-30) REVERT: B 658 GLU cc_start: 0.7509 (pt0) cc_final: 0.7275 (pt0) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2947 time to fit residues: 113.3347 Evaluate side-chains 282 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 410 ASN A 433 GLN A 548 ASN A 700 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.193203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.161630 restraints weight = 44949.995| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.82 r_work: 0.3937 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10492 Z= 0.174 Angle : 0.578 5.612 14226 Z= 0.311 Chirality : 0.041 0.180 1530 Planarity : 0.004 0.044 1796 Dihedral : 4.825 18.967 1364 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.81 % Allowed : 5.61 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.61 (0.23), residues: 1218 helix: -0.32 (0.24), residues: 434 sheet: -2.26 (0.38), residues: 160 loop : -1.21 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 413 TYR 0.013 0.001 TYR B 504 PHE 0.011 0.001 PHE A 513 TRP 0.015 0.002 TRP A 312 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00370 (10488) covalent geometry : angle 0.57807 (14218) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.76064 ( 8) hydrogen bonds : bond 0.05606 ( 338) hydrogen bonds : angle 5.78879 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 277 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.7721 (tmm) cc_final: 0.7398 (tmm) REVERT: A 315 MET cc_start: 0.7852 (tmm) cc_final: 0.7638 (ttm) REVERT: A 509 GLU cc_start: 0.7016 (tt0) cc_final: 0.6459 (tt0) REVERT: A 528 ASN cc_start: 0.8108 (p0) cc_final: 0.7766 (p0) REVERT: A 551 MET cc_start: 0.7749 (mmm) cc_final: 0.7340 (mmm) REVERT: A 574 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 603 ARG cc_start: 0.7551 (mtt-85) cc_final: 0.7242 (mtt-85) REVERT: A 641 LYS cc_start: 0.8475 (tptp) cc_final: 0.8155 (tptm) REVERT: B 187 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 197 ASP cc_start: 0.7841 (m-30) cc_final: 0.7562 (m-30) REVERT: B 436 GLU cc_start: 0.7664 (pm20) cc_final: 0.7386 (mp0) REVERT: B 445 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7429 (mp0) REVERT: B 548 ASN cc_start: 0.7872 (p0) cc_final: 0.7502 (p0) REVERT: B 559 MET cc_start: 0.6661 (ppp) cc_final: 0.5745 (ppp) REVERT: B 652 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 654 GLU cc_start: 0.7727 (mp0) cc_final: 0.7309 (mp0) REVERT: B 656 ASP cc_start: 0.7657 (m-30) cc_final: 0.7370 (m-30) REVERT: B 658 GLU cc_start: 0.7631 (pt0) cc_final: 0.7307 (pt0) REVERT: B 741 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8019 (ttp80) outliers start: 9 outliers final: 8 residues processed: 279 average time/residue: 0.2928 time to fit residues: 107.3855 Evaluate side-chains 280 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 272 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.190569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159674 restraints weight = 44840.784| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.74 r_work: 0.3911 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10492 Z= 0.240 Angle : 0.589 5.648 14226 Z= 0.318 Chirality : 0.041 0.176 1530 Planarity : 0.004 0.046 1796 Dihedral : 4.956 19.857 1364 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.90 % Allowed : 8.68 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.23), residues: 1218 helix: -0.32 (0.24), residues: 432 sheet: -2.66 (0.35), residues: 164 loop : -1.18 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 413 TYR 0.016 0.002 TYR B 350 PHE 0.014 0.001 PHE A 460 TRP 0.018 0.002 TRP A 312 HIS 0.011 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00504 (10488) covalent geometry : angle 0.58916 (14218) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.64862 ( 8) hydrogen bonds : bond 0.05214 ( 338) hydrogen bonds : angle 5.59036 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 288 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.7685 (tmm) cc_final: 0.7256 (tmm) REVERT: A 327 MET cc_start: 0.3858 (pmm) cc_final: 0.2479 (ptp) REVERT: A 367 GLU cc_start: 0.8179 (pm20) cc_final: 0.7661 (mp0) REVERT: A 496 GLU cc_start: 0.6942 (tp30) cc_final: 0.6543 (tm-30) REVERT: A 509 GLU cc_start: 0.7073 (tt0) cc_final: 0.6440 (tt0) REVERT: A 512 GLN cc_start: 0.7867 (tt0) cc_final: 0.7633 (tt0) REVERT: A 528 ASN cc_start: 0.8140 (p0) cc_final: 0.7763 (p0) REVERT: A 603 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.7253 (mtt-85) REVERT: A 732 GLU cc_start: 0.8268 (mp0) cc_final: 0.8054 (mp0) REVERT: B 187 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 197 ASP cc_start: 0.7854 (m-30) cc_final: 0.7583 (m-30) REVERT: B 436 GLU cc_start: 0.7651 (pm20) cc_final: 0.7421 (mp0) REVERT: B 445 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7504 (mp0) REVERT: B 548 ASN cc_start: 0.7931 (p0) cc_final: 0.7539 (p0) REVERT: B 559 MET cc_start: 0.6709 (ppp) cc_final: 0.5810 (ppp) REVERT: B 577 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7725 (mmm-85) REVERT: B 652 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 654 GLU cc_start: 0.7740 (mp0) cc_final: 0.7322 (mp0) REVERT: B 656 ASP cc_start: 0.7684 (m-30) cc_final: 0.7397 (m-30) REVERT: B 658 GLU cc_start: 0.7602 (pt0) cc_final: 0.7312 (pt0) outliers start: 10 outliers final: 7 residues processed: 290 average time/residue: 0.2958 time to fit residues: 113.6405 Evaluate side-chains 286 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 279 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.191805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.159955 restraints weight = 44502.185| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 3.92 r_work: 0.3918 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10492 Z= 0.155 Angle : 0.548 5.608 14226 Z= 0.291 Chirality : 0.040 0.167 1530 Planarity : 0.004 0.047 1796 Dihedral : 4.732 19.087 1364 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.27 % Allowed : 9.95 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.49 (0.23), residues: 1218 helix: -0.09 (0.25), residues: 432 sheet: -2.66 (0.35), residues: 164 loop : -1.08 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.014 0.001 TYR B 693 PHE 0.012 0.001 PHE A 734 TRP 0.015 0.001 TRP A 312 HIS 0.006 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00334 (10488) covalent geometry : angle 0.54812 (14218) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.57229 ( 8) hydrogen bonds : bond 0.04522 ( 338) hydrogen bonds : angle 5.18817 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 288 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8022 (ttpp) REVERT: A 305 ASP cc_start: 0.8128 (p0) cc_final: 0.7922 (p0) REVERT: A 327 MET cc_start: 0.3703 (pmm) cc_final: 0.2493 (ptp) REVERT: A 367 GLU cc_start: 0.8190 (pm20) cc_final: 0.7594 (mp0) REVERT: A 496 GLU cc_start: 0.6950 (tp30) cc_final: 0.6491 (tm-30) REVERT: A 512 GLN cc_start: 0.7897 (tt0) cc_final: 0.7579 (tt0) REVERT: A 528 ASN cc_start: 0.8118 (p0) cc_final: 0.7714 (p0) REVERT: A 603 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7356 (mtt-85) REVERT: A 641 LYS cc_start: 0.8507 (tptp) cc_final: 0.8190 (tptm) REVERT: B 187 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 197 ASP cc_start: 0.7974 (m-30) cc_final: 0.7647 (m-30) REVERT: B 223 MET cc_start: 0.7588 (tmm) cc_final: 0.7360 (tmm) REVERT: B 436 GLU cc_start: 0.7679 (pm20) cc_final: 0.7460 (mp0) REVERT: B 445 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7602 (mp0) REVERT: B 536 LYS cc_start: 0.8176 (mttt) cc_final: 0.7954 (mtpp) REVERT: B 548 ASN cc_start: 0.7783 (p0) cc_final: 0.7386 (p0) REVERT: B 559 MET cc_start: 0.6677 (ppp) cc_final: 0.5725 (ppp) REVERT: B 578 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8029 (mtpp) REVERT: B 652 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 654 GLU cc_start: 0.7692 (mp0) cc_final: 0.7201 (mp0) REVERT: B 656 ASP cc_start: 0.7692 (m-30) cc_final: 0.7386 (m-30) REVERT: B 658 GLU cc_start: 0.7634 (pt0) cc_final: 0.7324 (pt0) REVERT: B 741 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8042 (ttp80) outliers start: 14 outliers final: 10 residues processed: 290 average time/residue: 0.2685 time to fit residues: 104.5686 Evaluate side-chains 290 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 280 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 735 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.189873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158017 restraints weight = 44632.081| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.82 r_work: 0.3883 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10492 Z= 0.240 Angle : 0.587 5.474 14226 Z= 0.315 Chirality : 0.042 0.170 1530 Planarity : 0.004 0.050 1796 Dihedral : 4.951 20.020 1364 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.27 % Allowed : 11.48 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.65 (0.23), residues: 1218 helix: -0.21 (0.24), residues: 432 sheet: -2.80 (0.35), residues: 164 loop : -1.17 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.019 0.002 TYR A 350 PHE 0.018 0.001 PHE A 460 TRP 0.015 0.002 TRP B 316 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00503 (10488) covalent geometry : angle 0.58728 (14218) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.68531 ( 8) hydrogen bonds : bond 0.04705 ( 338) hydrogen bonds : angle 5.26432 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 283 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.3687 (pmm) cc_final: 0.2576 (ptp) REVERT: A 367 GLU cc_start: 0.8202 (pm20) cc_final: 0.7757 (mp0) REVERT: A 496 GLU cc_start: 0.7068 (tp30) cc_final: 0.6841 (tm-30) REVERT: A 512 GLN cc_start: 0.8006 (tt0) cc_final: 0.7698 (tt0) REVERT: A 528 ASN cc_start: 0.8147 (p0) cc_final: 0.7727 (p0) REVERT: A 603 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7432 (mtt-85) REVERT: A 641 LYS cc_start: 0.8556 (tptp) cc_final: 0.8257 (tptm) REVERT: B 187 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 197 ASP cc_start: 0.7939 (m-30) cc_final: 0.7652 (m-30) REVERT: B 223 MET cc_start: 0.7555 (tmm) cc_final: 0.7349 (tmm) REVERT: B 445 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7648 (mp0) REVERT: B 466 GLU cc_start: 0.7982 (tt0) cc_final: 0.7477 (tm-30) REVERT: B 536 LYS cc_start: 0.8200 (mttt) cc_final: 0.7954 (mtpp) REVERT: B 548 ASN cc_start: 0.7799 (p0) cc_final: 0.7399 (p0) REVERT: B 559 MET cc_start: 0.6725 (ppp) cc_final: 0.5834 (ppp) REVERT: B 577 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7685 (mmm-85) REVERT: B 578 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8088 (mtpp) REVERT: B 608 LYS cc_start: 0.8451 (tppp) cc_final: 0.7755 (tptp) REVERT: B 652 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7024 (mm-30) REVERT: B 654 GLU cc_start: 0.7753 (mp0) cc_final: 0.7292 (mp0) REVERT: B 656 ASP cc_start: 0.7742 (m-30) cc_final: 0.7452 (m-30) REVERT: B 658 GLU cc_start: 0.7632 (pt0) cc_final: 0.7322 (pt0) outliers start: 14 outliers final: 11 residues processed: 287 average time/residue: 0.2608 time to fit residues: 100.3494 Evaluate side-chains 289 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 278 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.190037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158754 restraints weight = 44362.770| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 3.77 r_work: 0.3897 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10492 Z= 0.211 Angle : 0.579 5.908 14226 Z= 0.309 Chirality : 0.041 0.170 1530 Planarity : 0.004 0.050 1796 Dihedral : 4.887 20.485 1364 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.54 % Allowed : 12.93 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.23), residues: 1218 helix: -0.25 (0.24), residues: 432 sheet: -2.74 (0.37), residues: 154 loop : -1.30 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.014 0.002 TYR A 504 PHE 0.014 0.001 PHE B 625 TRP 0.015 0.002 TRP B 316 HIS 0.005 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00443 (10488) covalent geometry : angle 0.57892 (14218) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.61066 ( 8) hydrogen bonds : bond 0.04488 ( 338) hydrogen bonds : angle 5.14853 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8543 (tp) cc_final: 0.8159 (tt) REVERT: A 327 MET cc_start: 0.3596 (pmm) cc_final: 0.2505 (ptp) REVERT: A 367 GLU cc_start: 0.8169 (pm20) cc_final: 0.7581 (mp0) REVERT: A 496 GLU cc_start: 0.7086 (tp30) cc_final: 0.6710 (tm-30) REVERT: A 512 GLN cc_start: 0.8011 (tt0) cc_final: 0.7705 (tt0) REVERT: A 528 ASN cc_start: 0.8183 (p0) cc_final: 0.7739 (p0) REVERT: A 603 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7401 (mtt-85) REVERT: A 641 LYS cc_start: 0.8497 (tptp) cc_final: 0.8213 (tptm) REVERT: A 738 MET cc_start: 0.7345 (tmm) cc_final: 0.6457 (tmm) REVERT: B 187 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 197 ASP cc_start: 0.7875 (m-30) cc_final: 0.7614 (m-30) REVERT: B 466 GLU cc_start: 0.7918 (tt0) cc_final: 0.7445 (tm-30) REVERT: B 536 LYS cc_start: 0.8218 (mttt) cc_final: 0.7931 (mtpp) REVERT: B 548 ASN cc_start: 0.7808 (p0) cc_final: 0.7359 (p0) REVERT: B 559 MET cc_start: 0.6666 (ppp) cc_final: 0.5845 (ppp) REVERT: B 578 LYS cc_start: 0.8281 (mtpp) cc_final: 0.8036 (mtpp) REVERT: B 608 LYS cc_start: 0.8470 (tppp) cc_final: 0.7809 (tptp) REVERT: B 652 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6971 (mm-30) REVERT: B 653 TRP cc_start: 0.8029 (t60) cc_final: 0.7699 (t60) REVERT: B 654 GLU cc_start: 0.7700 (mp0) cc_final: 0.7499 (mp0) REVERT: B 656 ASP cc_start: 0.7716 (m-30) cc_final: 0.7410 (m-30) REVERT: B 658 GLU cc_start: 0.7656 (pt0) cc_final: 0.7377 (pt0) REVERT: B 703 MET cc_start: 0.7551 (mtt) cc_final: 0.7339 (mtt) outliers start: 17 outliers final: 14 residues processed: 285 average time/residue: 0.2779 time to fit residues: 105.9277 Evaluate side-chains 294 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 280 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.191771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159931 restraints weight = 44815.763| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.88 r_work: 0.3914 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10492 Z= 0.133 Angle : 0.550 6.487 14226 Z= 0.291 Chirality : 0.040 0.160 1530 Planarity : 0.004 0.048 1796 Dihedral : 4.661 19.016 1364 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.36 % Allowed : 13.74 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.23), residues: 1218 helix: -0.07 (0.25), residues: 436 sheet: -2.58 (0.37), residues: 154 loop : -1.18 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.011 0.001 TYR B 670 PHE 0.015 0.001 PHE B 625 TRP 0.017 0.001 TRP B 276 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00292 (10488) covalent geometry : angle 0.55037 (14218) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.49943 ( 8) hydrogen bonds : bond 0.04080 ( 338) hydrogen bonds : angle 4.89803 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 287 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8092 (pm20) cc_final: 0.7886 (pm20) REVERT: A 327 MET cc_start: 0.3551 (pmm) cc_final: 0.2570 (ptp) REVERT: A 496 GLU cc_start: 0.7070 (tp30) cc_final: 0.6699 (tm-30) REVERT: A 512 GLN cc_start: 0.7977 (tt0) cc_final: 0.7660 (tt0) REVERT: A 528 ASN cc_start: 0.8162 (p0) cc_final: 0.7686 (p0) REVERT: A 551 MET cc_start: 0.7768 (mmm) cc_final: 0.7508 (mmm) REVERT: A 603 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7405 (mtt-85) REVERT: A 641 LYS cc_start: 0.8551 (tptp) cc_final: 0.8270 (tptm) REVERT: A 734 PHE cc_start: 0.8192 (t80) cc_final: 0.7882 (t80) REVERT: B 187 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 197 ASP cc_start: 0.7909 (m-30) cc_final: 0.7623 (m-30) REVERT: B 466 GLU cc_start: 0.7985 (tt0) cc_final: 0.7485 (tm-30) REVERT: B 536 LYS cc_start: 0.8214 (mttt) cc_final: 0.7884 (mtpp) REVERT: B 537 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 548 ASN cc_start: 0.7705 (p0) cc_final: 0.7297 (p0) REVERT: B 559 MET cc_start: 0.6629 (ppp) cc_final: 0.5792 (ppp) REVERT: B 578 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8035 (mtpp) REVERT: B 608 LYS cc_start: 0.8515 (tppp) cc_final: 0.7830 (tptp) REVERT: B 652 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 653 TRP cc_start: 0.7995 (t60) cc_final: 0.7739 (t60) REVERT: B 656 ASP cc_start: 0.7694 (m-30) cc_final: 0.7390 (m-30) REVERT: B 658 GLU cc_start: 0.7685 (pt0) cc_final: 0.7394 (pt0) REVERT: B 703 MET cc_start: 0.7517 (mtt) cc_final: 0.7271 (mtt) REVERT: B 741 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7801 (ttp80) outliers start: 15 outliers final: 13 residues processed: 290 average time/residue: 0.2769 time to fit residues: 107.1072 Evaluate side-chains 299 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 286 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 6.9990 chunk 111 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.189191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.157894 restraints weight = 45188.902| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.81 r_work: 0.3911 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10492 Z= 0.215 Angle : 0.584 6.863 14226 Z= 0.311 Chirality : 0.041 0.166 1530 Planarity : 0.004 0.050 1796 Dihedral : 4.843 19.688 1364 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.63 % Allowed : 14.83 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.66 (0.23), residues: 1218 helix: -0.15 (0.25), residues: 432 sheet: -2.70 (0.37), residues: 154 loop : -1.31 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.018 0.002 TYR B 693 PHE 0.015 0.001 PHE B 625 TRP 0.024 0.002 TRP B 276 HIS 0.006 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00452 (10488) covalent geometry : angle 0.58378 (14218) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.61300 ( 8) hydrogen bonds : bond 0.04356 ( 338) hydrogen bonds : angle 5.04591 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 291 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7260 (mtt90) REVERT: A 254 LEU cc_start: 0.8529 (tp) cc_final: 0.8140 (tt) REVERT: A 327 MET cc_start: 0.3633 (pmm) cc_final: 0.2765 (ptp) REVERT: A 496 GLU cc_start: 0.7191 (tp30) cc_final: 0.6833 (tm-30) REVERT: A 528 ASN cc_start: 0.8229 (p0) cc_final: 0.7767 (p0) REVERT: A 551 MET cc_start: 0.7710 (mmm) cc_final: 0.7479 (mmm) REVERT: A 558 TYR cc_start: 0.7558 (m-10) cc_final: 0.6683 (m-10) REVERT: A 603 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7455 (mtt-85) REVERT: A 641 LYS cc_start: 0.8552 (tptp) cc_final: 0.8287 (tptm) REVERT: A 734 PHE cc_start: 0.8179 (t80) cc_final: 0.7888 (t80) REVERT: B 187 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7922 (tm-30) REVERT: B 195 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: B 197 ASP cc_start: 0.7851 (m-30) cc_final: 0.7597 (m-30) REVERT: B 484 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7151 (mtm-85) REVERT: B 536 LYS cc_start: 0.8242 (mttt) cc_final: 0.7926 (mtpp) REVERT: B 548 ASN cc_start: 0.7816 (p0) cc_final: 0.7408 (p0) REVERT: B 559 MET cc_start: 0.6809 (ppp) cc_final: 0.5978 (ppp) REVERT: B 578 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7995 (mtpp) REVERT: B 608 LYS cc_start: 0.8499 (tppp) cc_final: 0.7823 (tptp) REVERT: B 652 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 653 TRP cc_start: 0.8055 (t60) cc_final: 0.7685 (t60) REVERT: B 656 ASP cc_start: 0.7721 (m-30) cc_final: 0.7442 (m-30) REVERT: B 658 GLU cc_start: 0.7655 (pt0) cc_final: 0.7384 (pt0) REVERT: B 692 GLU cc_start: 0.8068 (tt0) cc_final: 0.7719 (tt0) REVERT: B 740 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8197 (mtt90) outliers start: 18 outliers final: 14 residues processed: 292 average time/residue: 0.2831 time to fit residues: 110.4539 Evaluate side-chains 299 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 285 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 56 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.189167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157284 restraints weight = 45432.526| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.88 r_work: 0.3899 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10492 Z= 0.127 Angle : 0.575 10.204 14226 Z= 0.299 Chirality : 0.040 0.157 1530 Planarity : 0.004 0.048 1796 Dihedral : 4.602 18.684 1364 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.99 % Allowed : 15.55 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.24), residues: 1218 helix: -0.01 (0.25), residues: 436 sheet: -2.52 (0.37), residues: 154 loop : -1.14 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.014 0.001 TYR B 693 PHE 0.012 0.001 PHE B 460 TRP 0.029 0.001 TRP B 276 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00281 (10488) covalent geometry : angle 0.57544 (14218) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.52579 ( 8) hydrogen bonds : bond 0.03895 ( 338) hydrogen bonds : angle 4.88523 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 288 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7185 (ttm-80) REVERT: A 254 LEU cc_start: 0.8485 (tp) cc_final: 0.8095 (tt) REVERT: A 327 MET cc_start: 0.3643 (pmm) cc_final: 0.2785 (ptp) REVERT: A 496 GLU cc_start: 0.7171 (tp30) cc_final: 0.6929 (tm-30) REVERT: A 558 TYR cc_start: 0.7515 (m-10) cc_final: 0.6584 (m-10) REVERT: A 603 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7444 (mtt-85) REVERT: A 641 LYS cc_start: 0.8522 (tptp) cc_final: 0.8273 (tptm) REVERT: A 734 PHE cc_start: 0.8139 (t80) cc_final: 0.7839 (t80) REVERT: B 187 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 197 ASP cc_start: 0.7864 (m-30) cc_final: 0.7591 (m-30) REVERT: B 310 MET cc_start: 0.7978 (pmm) cc_final: 0.7718 (pmm) REVERT: B 536 LYS cc_start: 0.8266 (mttt) cc_final: 0.7959 (mtpp) REVERT: B 548 ASN cc_start: 0.7819 (p0) cc_final: 0.7368 (p0) REVERT: B 559 MET cc_start: 0.6736 (ppp) cc_final: 0.5898 (ppp) REVERT: B 577 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7696 (mmm-85) REVERT: B 578 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7888 (mtpp) REVERT: B 608 LYS cc_start: 0.8530 (tppp) cc_final: 0.7846 (tptp) REVERT: B 652 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7115 (mm-30) REVERT: B 653 TRP cc_start: 0.8056 (t60) cc_final: 0.7802 (t60) REVERT: B 656 ASP cc_start: 0.7660 (m-30) cc_final: 0.7391 (m-30) REVERT: B 658 GLU cc_start: 0.7616 (pt0) cc_final: 0.7358 (pt0) REVERT: B 672 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: B 692 GLU cc_start: 0.8038 (tt0) cc_final: 0.7709 (tt0) REVERT: B 741 ARG cc_start: 0.8256 (ttp80) cc_final: 0.8045 (ttp80) outliers start: 11 outliers final: 10 residues processed: 289 average time/residue: 0.2879 time to fit residues: 110.9591 Evaluate side-chains 296 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 286 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 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 = 0.4418 r_free = 0.4418 target = 0.187859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156713 restraints weight = 45369.162| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.82 r_work: 0.3886 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10492 Z= 0.164 Angle : 0.589 8.183 14226 Z= 0.309 Chirality : 0.040 0.158 1530 Planarity : 0.004 0.048 1796 Dihedral : 4.658 19.029 1364 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.99 % Allowed : 15.46 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.24), residues: 1218 helix: -0.00 (0.25), residues: 432 sheet: -2.56 (0.37), residues: 154 loop : -1.18 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 577 TYR 0.015 0.001 TYR B 693 PHE 0.018 0.001 PHE B 625 TRP 0.044 0.002 TRP A 679 HIS 0.005 0.001 HIS A 705 Details of bonding type rmsd covalent geometry : bond 0.00359 (10488) covalent geometry : angle 0.58902 (14218) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.55878 ( 8) hydrogen bonds : bond 0.04015 ( 338) hydrogen bonds : angle 4.97531 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 291 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7194 (mtt90) REVERT: A 254 LEU cc_start: 0.8498 (tp) cc_final: 0.8102 (tt) REVERT: A 327 MET cc_start: 0.3640 (pmm) cc_final: 0.2798 (ptp) REVERT: A 496 GLU cc_start: 0.7190 (tp30) cc_final: 0.6953 (tm-30) REVERT: A 558 TYR cc_start: 0.7537 (m-10) cc_final: 0.6623 (m-10) REVERT: A 603 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7460 (mtt-85) REVERT: A 641 LYS cc_start: 0.8526 (tptp) cc_final: 0.8286 (tptm) REVERT: A 734 PHE cc_start: 0.8128 (t80) cc_final: 0.7811 (t80) REVERT: B 187 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 197 ASP cc_start: 0.7875 (m-30) cc_final: 0.7607 (m-30) REVERT: B 536 LYS cc_start: 0.8278 (mttt) cc_final: 0.7822 (mtpp) REVERT: B 547 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7379 (ttm-80) REVERT: B 548 ASN cc_start: 0.7825 (p0) cc_final: 0.7219 (p0) REVERT: B 559 MET cc_start: 0.6743 (ppp) cc_final: 0.5922 (ppp) REVERT: B 578 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7900 (mtpp) REVERT: B 608 LYS cc_start: 0.8536 (tppp) cc_final: 0.7866 (tptp) REVERT: B 652 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 653 TRP cc_start: 0.8067 (t60) cc_final: 0.7680 (t60) REVERT: B 656 ASP cc_start: 0.7695 (m-30) cc_final: 0.7416 (m-30) REVERT: B 658 GLU cc_start: 0.7590 (pt0) cc_final: 0.7371 (pt0) REVERT: B 672 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: B 692 GLU cc_start: 0.8059 (tt0) cc_final: 0.7739 (tt0) outliers start: 11 outliers final: 10 residues processed: 291 average time/residue: 0.2921 time to fit residues: 113.0563 Evaluate side-chains 299 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 289 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 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 = 0.4433 r_free = 0.4433 target = 0.189251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156958 restraints weight = 45932.590| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.91 r_work: 0.3893 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10492 Z= 0.137 Angle : 0.592 13.294 14226 Z= 0.307 Chirality : 0.040 0.194 1530 Planarity : 0.004 0.048 1796 Dihedral : 4.581 20.225 1364 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.27 % Allowed : 15.19 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.37 (0.24), residues: 1218 helix: 0.08 (0.25), residues: 432 sheet: -2.51 (0.36), residues: 154 loop : -1.13 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.015 0.001 TYR B 693 PHE 0.019 0.001 PHE B 625 TRP 0.035 0.002 TRP A 679 HIS 0.016 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00307 (10488) covalent geometry : angle 0.59176 (14218) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.54650 ( 8) hydrogen bonds : bond 0.03866 ( 338) hydrogen bonds : angle 4.89451 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.07 seconds wall clock time: 85 minutes 7.90 seconds (5107.90 seconds total)