Starting phenix.real_space_refine on Thu Sep 18 02:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.map" model { file = "/net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jn9_61620/09_2025/9jn9_61620.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 100 5.16 5 C 8670 2.51 5 N 2306 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6775 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 38, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 6775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6775 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 38, 'TRANS': 807} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2072 SG CYS A 284 53.528 75.596 52.688 1.00 65.80 S ATOM 2346 SG CYS A 318 53.295 76.925 49.259 1.00 65.43 S ATOM 8847 SG CYS B 284 75.034 30.675 53.232 1.00 69.68 S ATOM 9121 SG CYS B 318 74.985 29.394 49.527 1.00 67.45 S Time building chain proxies: 3.08, per 1000 atoms: 0.23 Number of scatterers: 13552 At special positions: 0 Unit cell: (129.105, 106.875, 127.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 100 16.00 O 2474 8.00 N 2306 7.00 C 8670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.10 Conformation dependent library (CDL) restraints added in 466.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 282 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 318 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 284 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 284 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 318 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 282 " 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 17 sheets defined 38.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.543A pdb=" N MET A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 56 removed outlier: 3.628A pdb=" N LYS A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.501A pdb=" N HIS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.590A pdb=" N GLY A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.187A pdb=" N ILE A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 220 through 238 removed outlier: 3.642A pdb=" N ILE A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.524A pdb=" N ASN A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.111A pdb=" N GLU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 removed outlier: 4.047A pdb=" N VAL A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 removed outlier: 5.884A pdb=" N GLU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.630A pdb=" N CYS A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.595A pdb=" N HIS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 478 through 492 removed outlier: 4.018A pdb=" N LEU A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.553A pdb=" N MET A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 removed outlier: 4.120A pdb=" N CYS A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 569 " --> pdb=" O CYS A 565 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.134A pdb=" N GLU A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.574A pdb=" N MET A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.757A pdb=" N THR A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.766A pdb=" N ILE A 708 " --> pdb=" O PRO A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 750 removed outlier: 3.675A pdb=" N VAL A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.892A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 762 " --> pdb=" O PRO A 759 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 763 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 764 " --> pdb=" O THR A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 758 through 764' Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.921A pdb=" N TYR A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.778A pdb=" N HIS A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 799 through 804' Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.668A pdb=" N PHE A 894 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 34 through 56 removed outlier: 3.777A pdb=" N LYS B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.520A pdb=" N HIS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.892A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 238 removed outlier: 3.852A pdb=" N ILE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.666A pdb=" N SER B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.002A pdb=" N GLU B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.975A pdb=" N VAL B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 removed outlier: 5.812A pdb=" N GLU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.786A pdb=" N CYS B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.729A pdb=" N ILE B 428 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.954A pdb=" N LEU B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 537 through 553 removed outlier: 3.511A pdb=" N MET B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 584 removed outlier: 4.508A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 615 removed outlier: 3.993A pdb=" N ILE B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 674 through 682 removed outlier: 3.654A pdb=" N THR B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 Processing helix chain 'B' and resid 735 through 750 removed outlier: 3.763A pdb=" N LYS B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 748 " --> pdb=" O GLU B 744 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 763 removed outlier: 3.734A pdb=" N THR B 761 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 763 " --> pdb=" O ASP B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 758 through 763' Processing helix chain 'B' and resid 772 through 778 Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.619A pdb=" N ALA B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B 796 " --> pdb=" O GLN B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 799 through 803 removed outlier: 3.748A pdb=" N CYS B 802 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 809 removed outlier: 3.632A pdb=" N GLY B 809 " --> pdb=" O PHE B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 825 removed outlier: 3.615A pdb=" N ARG B 825 " --> pdb=" O GLY B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 841 removed outlier: 3.577A pdb=" N THR B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.645A pdb=" N PHE B 894 " --> pdb=" O HIS B 890 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 890 through 895' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.512A pdb=" N ASP A 97 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.808A pdb=" N VAL A 309 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404 removed outlier: 6.229A pdb=" N GLN A 403 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE A 438 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 439 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 457 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS A 456 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 404 removed outlier: 6.229A pdb=" N GLN A 403 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE A 438 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 439 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 457 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 468 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 659 through 660 removed outlier: 7.147A pdb=" N ILE A 659 " --> pdb=" O TRP A 700 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE A 702 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 589 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU A 703 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE A 591 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LYS A 726 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE A 590 " --> pdb=" O LYS A 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 735 removed outlier: 7.006A pdb=" N CYS A 734 " --> pdb=" O LEU A 779 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 782 through 784 removed outlier: 6.161A pdb=" N VAL A 782 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 874 " --> pdb=" O HIS A 901 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR A 903 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 876 " --> pdb=" O TYR A 903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 819 removed outlier: 5.963A pdb=" N ILE A 817 " --> pdb=" O ASP A 863 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.567A pdb=" N ASP B 97 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.709A pdb=" N VAL B 309 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 403 through 404 removed outlier: 6.371A pdb=" N GLN B 403 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 438 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS B 456 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 458 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 468 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 659 through 660 removed outlier: 7.141A pdb=" N ILE B 659 " --> pdb=" O TRP B 700 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHE B 702 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 589 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 703 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 591 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS B 726 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 590 " --> pdb=" O LYS B 726 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 622 through 624 Processing sheet with id=AB8, first strand: chain 'B' and resid 782 through 784 removed outlier: 6.279A pdb=" N VAL B 782 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 874 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR B 903 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 876 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 815 " --> pdb=" O VAL B 861 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP B 863 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE B 817 " --> pdb=" O ASP B 863 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1002 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: 1.62 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3287 1.33 - 1.45: 2621 1.45 - 1.57: 7788 1.57 - 1.69: 0 1.69 - 1.82: 142 Bond restraints: 13838 Sorted by residual: bond pdb=" N MET B 183 " pdb=" CA MET B 183 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.63e+00 bond pdb=" N LEU B 228 " pdb=" CA LEU B 228 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.41e-02 5.03e+03 8.25e+00 bond pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.41e-02 5.03e+03 7.46e+00 bond pdb=" N GLU A 421 " pdb=" CA GLU A 421 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.90e+00 bond pdb=" N GLU B 421 " pdb=" CA GLU B 421 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.40e+00 ... (remaining 13833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17834 2.12 - 4.24: 665 4.24 - 6.36: 124 6.36 - 8.48: 36 8.48 - 10.60: 13 Bond angle restraints: 18672 Sorted by residual: angle pdb=" N ASP B 182 " pdb=" CA ASP B 182 " pdb=" C ASP B 182 " ideal model delta sigma weight residual 110.53 100.98 9.55 1.29e+00 6.01e-01 5.48e+01 angle pdb=" N PRO B 229 " pdb=" CA PRO B 229 " pdb=" C PRO B 229 " ideal model delta sigma weight residual 113.81 105.23 8.58 1.45e+00 4.76e-01 3.50e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 114.39 105.94 8.45 1.45e+00 4.76e-01 3.40e+01 angle pdb=" CA ASP B 182 " pdb=" C ASP B 182 " pdb=" O ASP B 182 " ideal model delta sigma weight residual 121.94 115.53 6.41 1.15e+00 7.56e-01 3.11e+01 angle pdb=" C TYR B 770 " pdb=" N GLU B 771 " pdb=" CA GLU B 771 " ideal model delta sigma weight residual 121.54 132.14 -10.60 1.91e+00 2.74e-01 3.08e+01 ... (remaining 18667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7280 17.77 - 35.54: 914 35.54 - 53.31: 194 53.31 - 71.09: 45 71.09 - 88.86: 17 Dihedral angle restraints: 8450 sinusoidal: 3496 harmonic: 4954 Sorted by residual: dihedral pdb=" C LEU A 228 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta harmonic sigma weight residual -122.60 -142.13 19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta harmonic sigma weight residual 122.80 142.16 -19.36 0 2.50e+00 1.60e-01 6.00e+01 dihedral pdb=" C LEU B 228 " pdb=" N LEU B 228 " pdb=" CA LEU B 228 " pdb=" CB LEU B 228 " ideal model delta harmonic sigma weight residual -122.60 -137.82 15.22 0 2.50e+00 1.60e-01 3.71e+01 ... (remaining 8447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2067 0.159 - 0.318: 19 0.318 - 0.477: 0 0.477 - 0.636: 1 0.636 - 0.795: 1 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CA LEU A 228 " pdb=" N LEU A 228 " pdb=" C LEU A 228 " pdb=" CB LEU A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA LEU B 228 " pdb=" N LEU B 228 " pdb=" C LEU B 228 " pdb=" CB LEU B 228 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" CB ILE A 732 " pdb=" CA ILE A 732 " pdb=" CG1 ILE A 732 " pdb=" CG2 ILE A 732 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2085 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 227 " 0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C MET A 227 " -0.074 2.00e-02 2.50e+03 pdb=" O MET A 227 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A 228 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 718 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO B 719 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 719 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 719 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 683 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO B 684 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 684 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 684 " -0.042 5.00e-02 4.00e+02 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3497 2.80 - 3.33: 11514 3.33 - 3.85: 21360 3.85 - 4.38: 23684 4.38 - 4.90: 40611 Nonbonded interactions: 100666 Sorted by model distance: nonbonded pdb=" O ILE A 330 " pdb=" OG1 THR A 337 " model vdw 2.280 3.040 nonbonded pdb=" OG SER B 669 " pdb=" O VAL B 713 " model vdw 2.280 3.040 nonbonded pdb=" O ILE B 330 " pdb=" OG1 THR B 337 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 720 " pdb=" OG SER B 720 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 441 " pdb=" OH TYR A 484 " model vdw 2.318 3.040 ... (remaining 100661 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.090 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.310 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 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 : 0.010 0.693 13844 Z= 0.375 Angle : 1.019 10.597 18672 Z= 0.570 Chirality : 0.058 0.795 2088 Planarity : 0.008 0.077 2368 Dihedral : 16.719 88.856 5234 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.44 % Favored : 89.44 % Rotamer: Outliers : 0.99 % Allowed : 8.83 % Favored : 90.18 % Cbeta Deviations : 0.12 % 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 aren not related in a simple way. whole: -4.81 (0.16), residues: 1676 helix: -3.45 (0.14), residues: 536 sheet: -2.67 (0.28), residues: 250 loop : -3.23 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 843 TYR 0.016 0.002 TYR A 623 PHE 0.030 0.002 PHE A 215 TRP 0.023 0.002 TRP B 674 HIS 0.008 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00479 (13838) covalent geometry : angle 1.01930 (18672) hydrogen bonds : bond 0.20279 ( 346) hydrogen bonds : angle 8.32888 ( 1002) metal coordination : bond 0.40651 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 SER cc_start: 0.7805 (m) cc_final: 0.7564 (p) REVERT: A 268 LYS cc_start: 0.7938 (tptp) cc_final: 0.7546 (ttpp) REVERT: A 385 LYS cc_start: 0.8035 (tttt) cc_final: 0.7817 (tttt) REVERT: A 391 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 648 PHE cc_start: 0.4959 (t80) cc_final: 0.4174 (t80) REVERT: A 723 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5862 (m-10) REVERT: A 770 TYR cc_start: 0.7611 (m-10) cc_final: 0.7404 (m-80) REVERT: A 836 MET cc_start: 0.5331 (mmt) cc_final: 0.4904 (mmt) REVERT: A 861 VAL cc_start: 0.7949 (t) cc_final: 0.7695 (t) REVERT: A 877 PHE cc_start: 0.6804 (m-80) cc_final: 0.6442 (m-80) REVERT: B 183 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4276 (ttp) REVERT: B 207 SER cc_start: 0.7921 (p) cc_final: 0.7381 (m) REVERT: B 288 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: B 437 ILE cc_start: 0.7548 (mm) cc_final: 0.7181 (mt) REVERT: B 499 VAL cc_start: 0.7997 (t) cc_final: 0.7730 (m) REVERT: B 543 ASP cc_start: 0.6994 (t0) cc_final: 0.6744 (t0) REVERT: B 648 PHE cc_start: 0.4726 (t80) cc_final: 0.3713 (t80) REVERT: B 653 PHE cc_start: 0.6726 (m-80) cc_final: 0.6526 (m-80) REVERT: B 836 MET cc_start: 0.5211 (mmt) cc_final: 0.4891 (mmt) outliers start: 15 outliers final: 4 residues processed: 292 average time/residue: 0.1243 time to fit residues: 51.9614 Evaluate side-chains 259 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 263 ASN A 282 HIS A 452 GLN A 487 ASN A 575 GLN A 641 GLN A 680 ASN B 28 ASN B 93 GLN B 393 HIS B 417 HIS B 673 ASN B 680 ASN B 901 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.196586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.177191 restraints weight = 20748.695| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.86 r_work: 0.4141 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 2.335 13844 Z= 0.672 Angle : 0.631 11.922 18672 Z= 0.323 Chirality : 0.043 0.192 2088 Planarity : 0.006 0.067 2368 Dihedral : 5.860 55.115 1827 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.13 % Favored : 90.81 % Rotamer: Outliers : 2.11 % Allowed : 14.36 % Favored : 83.53 % 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 aren not related in a simple way. whole: -3.68 (0.18), residues: 1676 helix: -2.16 (0.19), residues: 572 sheet: -2.29 (0.30), residues: 236 loop : -2.70 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 534 TYR 0.025 0.001 TYR B 484 PHE 0.017 0.001 PHE B 448 TRP 0.018 0.001 TRP B 674 HIS 0.010 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00268 (13838) covalent geometry : angle 0.63149 (18672) hydrogen bonds : bond 0.04002 ( 346) hydrogen bonds : angle 5.76361 ( 1002) metal coordination : bond 0.95330 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7201 (mmt90) REVERT: A 49 ILE cc_start: 0.7917 (mm) cc_final: 0.7607 (mt) REVERT: A 133 ARG cc_start: 0.7248 (tpt90) cc_final: 0.6991 (tpt90) REVERT: A 207 SER cc_start: 0.7918 (m) cc_final: 0.7467 (p) REVERT: A 215 PHE cc_start: 0.6776 (p90) cc_final: 0.6514 (p90) REVERT: A 268 LYS cc_start: 0.8085 (tptp) cc_final: 0.7666 (ttpp) REVERT: A 449 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7800 (ttp80) REVERT: A 452 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5749 (pp30) REVERT: A 543 ASP cc_start: 0.7076 (t0) cc_final: 0.6863 (t0) REVERT: A 563 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.5820 (mpp) REVERT: A 648 PHE cc_start: 0.5447 (t80) cc_final: 0.4539 (t80) REVERT: A 655 LYS cc_start: 0.6086 (tppt) cc_final: 0.5856 (tppt) REVERT: A 723 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6476 (m-10) REVERT: A 742 MET cc_start: 0.6617 (mmt) cc_final: 0.6383 (mmt) REVERT: A 770 TYR cc_start: 0.7517 (m-10) cc_final: 0.7257 (m-80) REVERT: A 836 MET cc_start: 0.5547 (mmt) cc_final: 0.4976 (mmt) REVERT: A 837 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5542 (mp0) REVERT: A 877 PHE cc_start: 0.6896 (m-80) cc_final: 0.6550 (m-80) REVERT: B 207 SER cc_start: 0.7914 (p) cc_final: 0.7566 (m) REVERT: B 534 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7211 (mtm-85) REVERT: B 648 PHE cc_start: 0.4863 (t80) cc_final: 0.3643 (t80) REVERT: B 877 PHE cc_start: 0.7110 (m-80) cc_final: 0.6786 (m-80) outliers start: 32 outliers final: 14 residues processed: 274 average time/residue: 0.1306 time to fit residues: 50.9075 Evaluate side-chains 265 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 817 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 101 GLN A 452 GLN A 491 GLN A 866 GLN B 54 ASN B 93 GLN B 101 GLN B 393 HIS B 641 GLN B 696 HIS B 901 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.191981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.172295 restraints weight = 20804.848| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.87 r_work: 0.4094 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13844 Z= 0.166 Angle : 0.655 12.374 18672 Z= 0.336 Chirality : 0.045 0.185 2088 Planarity : 0.006 0.062 2368 Dihedral : 5.633 39.195 1819 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 2.90 % Allowed : 17.13 % Favored : 79.97 % 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 aren not related in a simple way. whole: -3.35 (0.18), residues: 1676 helix: -1.76 (0.19), residues: 600 sheet: -2.14 (0.30), residues: 236 loop : -2.60 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 449 TYR 0.018 0.002 TYR B 484 PHE 0.015 0.002 PHE B 653 TRP 0.021 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00376 (13838) covalent geometry : angle 0.65534 (18672) hydrogen bonds : bond 0.04360 ( 346) hydrogen bonds : angle 5.50854 ( 1002) metal coordination : bond 0.03611 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.7281 (tpt90) cc_final: 0.7035 (tpt170) REVERT: A 213 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6874 (ttpt) REVERT: A 215 PHE cc_start: 0.6836 (p90) cc_final: 0.6590 (p90) REVERT: A 268 LYS cc_start: 0.8143 (tptp) cc_final: 0.7652 (ttpp) REVERT: A 385 LYS cc_start: 0.8314 (tttt) cc_final: 0.8086 (tttt) REVERT: A 452 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.5540 (pp30) REVERT: A 563 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.5950 (mpp) REVERT: A 655 LYS cc_start: 0.6276 (tppt) cc_final: 0.5994 (tppt) REVERT: A 723 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: A 770 TYR cc_start: 0.7497 (m-10) cc_final: 0.7132 (m-80) REVERT: A 788 ASN cc_start: 0.7597 (t0) cc_final: 0.7375 (t0) REVERT: A 836 MET cc_start: 0.5673 (mmt) cc_final: 0.5066 (mmt) REVERT: A 837 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5416 (mp0) REVERT: B 131 TYR cc_start: 0.7121 (m-80) cc_final: 0.6888 (m-80) REVERT: B 207 SER cc_start: 0.8039 (p) cc_final: 0.7603 (m) REVERT: B 427 LEU cc_start: 0.8386 (tp) cc_final: 0.8121 (tt) REVERT: B 534 ARG cc_start: 0.7435 (mtm110) cc_final: 0.7161 (mtm-85) REVERT: B 577 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7929 (tp40) REVERT: B 836 MET cc_start: 0.5327 (mmt) cc_final: 0.4534 (mmt) REVERT: B 877 PHE cc_start: 0.7208 (m-80) cc_final: 0.6816 (m-80) outliers start: 44 outliers final: 24 residues processed: 270 average time/residue: 0.1304 time to fit residues: 50.3684 Evaluate side-chains 266 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 149 optimal weight: 0.0980 chunk 107 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 138 optimal weight: 0.0970 chunk 159 optimal weight: 5.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 733 HIS B 54 ASN B 393 HIS B 641 GLN B 733 HIS B 777 GLN B 901 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.195941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.176255 restraints weight = 20915.771| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.89 r_work: 0.4142 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13844 Z= 0.106 Angle : 0.604 13.428 18672 Z= 0.301 Chirality : 0.043 0.184 2088 Planarity : 0.005 0.058 2368 Dihedral : 5.148 41.190 1818 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 2.83 % Allowed : 18.45 % Favored : 78.72 % 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 aren not related in a simple way. whole: -2.77 (0.19), residues: 1676 helix: -1.20 (0.21), residues: 572 sheet: -1.87 (0.31), residues: 232 loop : -2.28 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 449 TYR 0.016 0.001 TYR B 484 PHE 0.017 0.001 PHE B 653 TRP 0.025 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00235 (13838) covalent geometry : angle 0.60362 (18672) hydrogen bonds : bond 0.03270 ( 346) hydrogen bonds : angle 5.04000 ( 1002) metal coordination : bond 0.02730 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.7236 (tpt90) cc_final: 0.6974 (tpt90) REVERT: A 213 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6847 (ttpt) REVERT: A 215 PHE cc_start: 0.6731 (p90) cc_final: 0.6490 (p90) REVERT: A 268 LYS cc_start: 0.8083 (tptp) cc_final: 0.7681 (ttpp) REVERT: A 385 LYS cc_start: 0.8261 (tttt) cc_final: 0.8042 (tttt) REVERT: A 449 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7701 (ttp80) REVERT: A 452 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5561 (pp30) REVERT: A 563 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.5844 (mpp) REVERT: A 648 PHE cc_start: 0.5514 (t80) cc_final: 0.4440 (t80) REVERT: A 655 LYS cc_start: 0.6158 (tppt) cc_final: 0.5914 (tppt) REVERT: A 723 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: A 751 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 788 ASN cc_start: 0.7553 (t0) cc_final: 0.7332 (t0) REVERT: A 836 MET cc_start: 0.5586 (mmt) cc_final: 0.4990 (mmt) REVERT: A 837 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5394 (mp0) REVERT: A 877 PHE cc_start: 0.6979 (m-80) cc_final: 0.6462 (m-80) REVERT: B 207 SER cc_start: 0.7829 (p) cc_final: 0.7364 (m) REVERT: B 227 MET cc_start: 0.4482 (OUTLIER) cc_final: 0.4257 (ttp) REVERT: B 427 LEU cc_start: 0.8307 (tp) cc_final: 0.8046 (tt) REVERT: B 648 PHE cc_start: 0.4894 (t80) cc_final: 0.3723 (t80) REVERT: B 659 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (pt) REVERT: B 836 MET cc_start: 0.5241 (mmt) cc_final: 0.4613 (mmt) REVERT: B 877 PHE cc_start: 0.7194 (m-80) cc_final: 0.6770 (m-80) outliers start: 43 outliers final: 16 residues processed: 263 average time/residue: 0.1255 time to fit residues: 47.1984 Evaluate side-chains 258 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 815 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 0.0040 chunk 6 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 452 GLN B 54 ASN B 641 GLN B 777 GLN B 901 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.193913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.174076 restraints weight = 20750.580| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.85 r_work: 0.4121 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13844 Z= 0.126 Angle : 0.619 12.653 18672 Z= 0.308 Chirality : 0.043 0.184 2088 Planarity : 0.005 0.059 2368 Dihedral : 5.126 41.630 1818 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer: Outliers : 3.23 % Allowed : 19.30 % Favored : 77.47 % 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 aren not related in a simple way. whole: -2.61 (0.20), residues: 1676 helix: -1.02 (0.21), residues: 586 sheet: -1.81 (0.32), residues: 236 loop : -2.23 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 534 TYR 0.014 0.001 TYR B 484 PHE 0.015 0.001 PHE B 653 TRP 0.031 0.001 TRP B 674 HIS 0.018 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00285 (13838) covalent geometry : angle 0.61943 (18672) hydrogen bonds : bond 0.03552 ( 346) hydrogen bonds : angle 5.02984 ( 1002) metal coordination : bond 0.02557 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7928 (mm) cc_final: 0.7678 (mp) REVERT: A 183 MET cc_start: 0.5135 (tpp) cc_final: 0.4465 (ttt) REVERT: A 213 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6874 (ttpt) REVERT: A 215 PHE cc_start: 0.6754 (p90) cc_final: 0.6534 (p90) REVERT: A 268 LYS cc_start: 0.8128 (tptp) cc_final: 0.7676 (ttpp) REVERT: A 385 LYS cc_start: 0.8292 (tttt) cc_final: 0.8074 (tttt) REVERT: A 397 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7998 (m) REVERT: A 399 GLN cc_start: 0.7516 (mp10) cc_final: 0.7087 (mp10) REVERT: A 452 GLN cc_start: 0.5950 (OUTLIER) cc_final: 0.5327 (pp30) REVERT: A 474 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 563 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.5788 (mpp) REVERT: A 648 PHE cc_start: 0.5576 (t80) cc_final: 0.4539 (t80) REVERT: A 655 LYS cc_start: 0.6276 (tppt) cc_final: 0.6005 (tppt) REVERT: A 723 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6271 (m-10) REVERT: A 751 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: A 836 MET cc_start: 0.5626 (mmt) cc_final: 0.5042 (mmt) REVERT: A 877 PHE cc_start: 0.7025 (m-80) cc_final: 0.6584 (m-80) REVERT: B 207 SER cc_start: 0.7950 (p) cc_final: 0.7562 (m) REVERT: B 227 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.4140 (ttp) REVERT: B 648 PHE cc_start: 0.4967 (t80) cc_final: 0.3745 (t80) REVERT: B 665 GLU cc_start: 0.7314 (mp0) cc_final: 0.7046 (mp0) REVERT: B 771 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5789 (pt0) REVERT: B 836 MET cc_start: 0.5290 (mmt) cc_final: 0.4660 (mmt) REVERT: B 877 PHE cc_start: 0.7230 (m-80) cc_final: 0.6804 (m-80) outliers start: 49 outliers final: 23 residues processed: 259 average time/residue: 0.1302 time to fit residues: 47.7327 Evaluate side-chains 258 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 815 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 153 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 54 ASN B 393 HIS B 777 GLN B 901 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.193863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173995 restraints weight = 20654.014| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.85 r_work: 0.4120 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13844 Z= 0.122 Angle : 0.625 12.527 18672 Z= 0.307 Chirality : 0.044 0.189 2088 Planarity : 0.005 0.060 2368 Dihedral : 5.090 42.308 1818 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.36 % Allowed : 19.24 % Favored : 77.40 % 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 aren not related in a simple way. whole: -2.47 (0.20), residues: 1676 helix: -0.83 (0.21), residues: 598 sheet: -1.75 (0.32), residues: 236 loop : -2.22 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 534 TYR 0.014 0.001 TYR B 484 PHE 0.018 0.001 PHE B 653 TRP 0.023 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00276 (13838) covalent geometry : angle 0.62465 (18672) hydrogen bonds : bond 0.03433 ( 346) hydrogen bonds : angle 4.99646 ( 1002) metal coordination : bond 0.02413 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7909 (mm) cc_final: 0.7654 (mp) REVERT: A 213 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6877 (ttpt) REVERT: A 215 PHE cc_start: 0.6820 (p90) cc_final: 0.6566 (p90) REVERT: A 268 LYS cc_start: 0.8110 (tptp) cc_final: 0.7721 (ttpp) REVERT: A 306 ASP cc_start: 0.3608 (OUTLIER) cc_final: 0.0166 (m-30) REVERT: A 385 LYS cc_start: 0.8290 (tttt) cc_final: 0.8071 (tttt) REVERT: A 397 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 399 GLN cc_start: 0.7511 (mp10) cc_final: 0.7016 (mp10) REVERT: A 563 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.5754 (mpp) REVERT: A 648 PHE cc_start: 0.5610 (t80) cc_final: 0.4476 (t80) REVERT: A 655 LYS cc_start: 0.6317 (tppt) cc_final: 0.6063 (tppt) REVERT: A 723 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.6292 (m-10) REVERT: A 750 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8444 (tttt) REVERT: A 751 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: A 836 MET cc_start: 0.5647 (mmt) cc_final: 0.5032 (mmt) REVERT: A 877 PHE cc_start: 0.7018 (m-80) cc_final: 0.6551 (m-80) REVERT: B 207 SER cc_start: 0.7894 (p) cc_final: 0.7570 (m) REVERT: B 227 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.4127 (ttp) REVERT: B 648 PHE cc_start: 0.5005 (t80) cc_final: 0.3790 (t80) REVERT: B 665 GLU cc_start: 0.7335 (mp0) cc_final: 0.7073 (mp0) REVERT: B 771 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5787 (pt0) REVERT: B 836 MET cc_start: 0.5266 (mmt) cc_final: 0.4635 (mmt) REVERT: B 877 PHE cc_start: 0.7200 (m-80) cc_final: 0.6790 (m-80) outliers start: 51 outliers final: 27 residues processed: 268 average time/residue: 0.1291 time to fit residues: 49.2090 Evaluate side-chains 266 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 815 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 165 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 452 GLN A 901 HIS B 54 ASN B 491 GLN B 777 GLN B 901 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.197052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.177390 restraints weight = 20884.978| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.88 r_work: 0.4158 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13844 Z= 0.099 Angle : 0.596 12.794 18672 Z= 0.292 Chirality : 0.042 0.180 2088 Planarity : 0.005 0.061 2368 Dihedral : 4.790 43.361 1818 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.90 % Allowed : 20.42 % Favored : 76.68 % 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 aren not related in a simple way. whole: -2.17 (0.20), residues: 1676 helix: -0.50 (0.22), residues: 598 sheet: -1.44 (0.34), residues: 230 loop : -2.15 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 534 TYR 0.022 0.001 TYR B 69 PHE 0.019 0.001 PHE B 653 TRP 0.033 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00220 (13838) covalent geometry : angle 0.59641 (18672) hydrogen bonds : bond 0.02711 ( 346) hydrogen bonds : angle 4.72301 ( 1002) metal coordination : bond 0.02122 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6815 (ttpt) REVERT: A 215 PHE cc_start: 0.6753 (p90) cc_final: 0.6518 (p90) REVERT: A 268 LYS cc_start: 0.8105 (tptp) cc_final: 0.7664 (ttpp) REVERT: A 306 ASP cc_start: 0.3673 (OUTLIER) cc_final: 0.0086 (m-30) REVERT: A 385 LYS cc_start: 0.8234 (tttt) cc_final: 0.8023 (tttt) REVERT: A 397 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 399 GLN cc_start: 0.7461 (mp10) cc_final: 0.6942 (mp10) REVERT: A 452 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5946 (pp30) REVERT: A 563 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.5730 (mpp) REVERT: A 648 PHE cc_start: 0.5405 (t80) cc_final: 0.4341 (t80) REVERT: A 655 LYS cc_start: 0.6223 (tppt) cc_final: 0.6013 (tppt) REVERT: A 723 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: A 750 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8443 (tttt) REVERT: A 751 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 770 TYR cc_start: 0.7365 (m-10) cc_final: 0.7113 (m-80) REVERT: A 836 MET cc_start: 0.5559 (mmt) cc_final: 0.4959 (mmt) REVERT: B 15 VAL cc_start: 0.6572 (t) cc_final: 0.6266 (p) REVERT: B 99 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4695 (mpp) REVERT: B 101 GLN cc_start: 0.7886 (mt0) cc_final: 0.7656 (mt0) REVERT: B 427 LEU cc_start: 0.8264 (tp) cc_final: 0.8016 (tt) REVERT: B 471 THR cc_start: 0.6399 (m) cc_final: 0.5598 (p) REVERT: B 588 GLU cc_start: 0.6365 (mp0) cc_final: 0.5939 (pm20) REVERT: B 648 PHE cc_start: 0.4866 (t80) cc_final: 0.3783 (t80) REVERT: B 836 MET cc_start: 0.5200 (mmt) cc_final: 0.4610 (mmt) outliers start: 44 outliers final: 21 residues processed: 267 average time/residue: 0.1251 time to fit residues: 48.0472 Evaluate side-chains 258 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 815 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 0.0270 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 393 HIS B 901 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.196123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.176395 restraints weight = 20673.064| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.87 r_work: 0.4144 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13844 Z= 0.111 Angle : 0.615 12.688 18672 Z= 0.304 Chirality : 0.043 0.182 2088 Planarity : 0.005 0.062 2368 Dihedral : 4.840 43.248 1818 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.64 % Allowed : 20.42 % Favored : 76.94 % 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 aren not related in a simple way. whole: -2.06 (0.21), residues: 1676 helix: -0.42 (0.22), residues: 598 sheet: -1.34 (0.34), residues: 230 loop : -2.09 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 534 TYR 0.013 0.001 TYR B 484 PHE 0.017 0.001 PHE B 653 TRP 0.027 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00251 (13838) covalent geometry : angle 0.61494 (18672) hydrogen bonds : bond 0.02982 ( 346) hydrogen bonds : angle 4.78975 ( 1002) metal coordination : bond 0.02210 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6876 (ttpt) REVERT: A 215 PHE cc_start: 0.6810 (p90) cc_final: 0.6556 (p90) REVERT: A 268 LYS cc_start: 0.8088 (tptp) cc_final: 0.7621 (ttpp) REVERT: A 306 ASP cc_start: 0.3599 (OUTLIER) cc_final: -0.0517 (m-30) REVERT: A 331 MET cc_start: 0.6083 (ppp) cc_final: 0.5835 (ppp) REVERT: A 385 LYS cc_start: 0.8286 (tttt) cc_final: 0.8067 (tttt) REVERT: A 397 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7980 (m) REVERT: A 399 GLN cc_start: 0.7464 (mp10) cc_final: 0.7068 (mp10) REVERT: A 563 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.5747 (mpp) REVERT: A 648 PHE cc_start: 0.5461 (t80) cc_final: 0.4414 (t80) REVERT: A 655 LYS cc_start: 0.6282 (tppt) cc_final: 0.6023 (tppt) REVERT: A 723 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: A 750 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8399 (tttt) REVERT: A 751 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: B 99 MET cc_start: 0.5293 (tpp) cc_final: 0.5076 (mpp) REVERT: B 101 GLN cc_start: 0.7905 (mt0) cc_final: 0.7638 (mt0) REVERT: B 427 LEU cc_start: 0.8245 (tp) cc_final: 0.8013 (tt) REVERT: B 588 GLU cc_start: 0.6424 (mp0) cc_final: 0.5943 (pm20) REVERT: B 648 PHE cc_start: 0.4790 (t80) cc_final: 0.3746 (t80) REVERT: B 836 MET cc_start: 0.5198 (mmt) cc_final: 0.4592 (mmt) outliers start: 40 outliers final: 26 residues processed: 257 average time/residue: 0.1256 time to fit residues: 46.2006 Evaluate side-chains 261 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 17 optimal weight: 0.0570 chunk 114 optimal weight: 0.0020 chunk 14 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.3306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 452 GLN B 54 ASN B 239 GLN B 393 HIS B 901 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.197291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177578 restraints weight = 20876.100| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.91 r_work: 0.4162 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13844 Z= 0.104 Angle : 0.610 12.819 18672 Z= 0.299 Chirality : 0.043 0.178 2088 Planarity : 0.005 0.062 2368 Dihedral : 4.770 43.510 1818 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.31 % Allowed : 21.34 % Favored : 76.35 % 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 aren not related in a simple way. whole: -1.94 (0.21), residues: 1676 helix: -0.31 (0.22), residues: 598 sheet: -1.25 (0.34), residues: 230 loop : -2.04 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 534 TYR 0.012 0.001 TYR B 484 PHE 0.018 0.001 PHE B 653 TRP 0.025 0.001 TRP B 674 HIS 0.016 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00235 (13838) covalent geometry : angle 0.60977 (18672) hydrogen bonds : bond 0.02729 ( 346) hydrogen bonds : angle 4.68019 ( 1002) metal coordination : bond 0.02077 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6213 (t) REVERT: A 213 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6845 (ttpt) REVERT: A 215 PHE cc_start: 0.6780 (p90) cc_final: 0.6538 (p90) REVERT: A 268 LYS cc_start: 0.8098 (tptp) cc_final: 0.7705 (ttpp) REVERT: A 306 ASP cc_start: 0.3514 (OUTLIER) cc_final: -0.0426 (m-30) REVERT: A 331 MET cc_start: 0.6067 (ppp) cc_final: 0.5856 (ppp) REVERT: A 385 LYS cc_start: 0.8272 (tttt) cc_final: 0.8048 (tttt) REVERT: A 397 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8072 (m) REVERT: A 399 GLN cc_start: 0.7579 (mp10) cc_final: 0.7004 (mp10) REVERT: A 452 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.5971 (pp30) REVERT: A 563 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.5670 (mpp) REVERT: A 648 PHE cc_start: 0.5354 (t80) cc_final: 0.4272 (t80) REVERT: A 655 LYS cc_start: 0.6246 (tppt) cc_final: 0.5945 (tppt) REVERT: A 723 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: A 750 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8376 (tttt) REVERT: A 751 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 99 MET cc_start: 0.5166 (OUTLIER) cc_final: 0.4939 (mpp) REVERT: B 101 GLN cc_start: 0.7945 (mt0) cc_final: 0.7669 (mt0) REVERT: B 588 GLU cc_start: 0.6379 (mp0) cc_final: 0.5951 (pm20) REVERT: B 648 PHE cc_start: 0.4601 (t80) cc_final: 0.3643 (t80) REVERT: B 836 MET cc_start: 0.5118 (mmt) cc_final: 0.4538 (mmt) outliers start: 35 outliers final: 21 residues processed: 253 average time/residue: 0.1297 time to fit residues: 46.9853 Evaluate side-chains 256 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 0.0370 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 239 GLN B 393 HIS B 901 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.194108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174204 restraints weight = 20547.689| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.89 r_work: 0.4117 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13844 Z= 0.149 Angle : 0.667 12.674 18672 Z= 0.330 Chirality : 0.045 0.183 2088 Planarity : 0.005 0.065 2368 Dihedral : 5.054 43.058 1818 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.24 % Allowed : 21.61 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.21), residues: 1676 helix: -0.51 (0.22), residues: 598 sheet: -1.37 (0.33), residues: 236 loop : -2.04 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 534 TYR 0.014 0.002 TYR A 623 PHE 0.016 0.001 PHE B 653 TRP 0.021 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00342 (13838) covalent geometry : angle 0.66682 (18672) hydrogen bonds : bond 0.03535 ( 346) hydrogen bonds : angle 4.86841 ( 1002) metal coordination : bond 0.02388 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.6322 (t) REVERT: A 213 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6907 (ttpt) REVERT: A 215 PHE cc_start: 0.6853 (p90) cc_final: 0.6613 (p90) REVERT: A 268 LYS cc_start: 0.8204 (tptp) cc_final: 0.7779 (ttpp) REVERT: A 306 ASP cc_start: 0.3518 (OUTLIER) cc_final: 0.0038 (m-30) REVERT: A 329 TRP cc_start: 0.7004 (t-100) cc_final: 0.6693 (t60) REVERT: A 385 LYS cc_start: 0.8357 (tttt) cc_final: 0.8148 (tttt) REVERT: A 397 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8093 (m) REVERT: A 399 GLN cc_start: 0.7570 (mp10) cc_final: 0.7016 (mp10) REVERT: A 563 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5779 (mpp) REVERT: A 648 PHE cc_start: 0.5600 (t80) cc_final: 0.4414 (t80) REVERT: A 655 LYS cc_start: 0.6376 (tppt) cc_final: 0.6060 (tppt) REVERT: A 723 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: A 750 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8372 (tttt) REVERT: A 751 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 99 MET cc_start: 0.5521 (tpp) cc_final: 0.5290 (mpp) REVERT: B 101 GLN cc_start: 0.7971 (mt0) cc_final: 0.7711 (mt0) REVERT: B 589 LEU cc_start: 0.6856 (tp) cc_final: 0.6650 (tp) REVERT: B 648 PHE cc_start: 0.4949 (t80) cc_final: 0.3874 (t80) REVERT: B 836 MET cc_start: 0.5295 (mmt) cc_final: 0.4675 (mmt) REVERT: B 877 PHE cc_start: 0.7005 (m-80) cc_final: 0.6786 (m-80) outliers start: 34 outliers final: 24 residues processed: 252 average time/residue: 0.1313 time to fit residues: 47.2444 Evaluate side-chains 257 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 837 GLU Chi-restraints excluded: chain B residue 284 CYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 723 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 100 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 452 GLN B 54 ASN B 393 HIS B 901 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.194417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174477 restraints weight = 20853.592| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.90 r_work: 0.4124 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13844 Z= 0.131 Angle : 0.655 12.794 18672 Z= 0.323 Chirality : 0.044 0.179 2088 Planarity : 0.005 0.065 2368 Dihedral : 5.070 43.104 1818 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.44 % Allowed : 21.15 % Favored : 76.42 % 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 aren not related in a simple way. whole: -2.08 (0.21), residues: 1676 helix: -0.47 (0.22), residues: 590 sheet: -1.41 (0.33), residues: 236 loop : -2.04 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 534 TYR 0.014 0.001 TYR B 484 PHE 0.017 0.001 PHE B 653 TRP 0.023 0.001 TRP B 674 HIS 0.017 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00299 (13838) covalent geometry : angle 0.65491 (18672) hydrogen bonds : bond 0.03340 ( 346) hydrogen bonds : angle 4.82829 ( 1002) metal coordination : bond 0.02240 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.98 seconds wall clock time: 51 minutes 19.94 seconds (3079.94 seconds total)