Starting phenix.real_space_refine on Sat Sep 12 05:02:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.cif Found real_map, /net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.map" model { file = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6que_4637/09_2026/6que_4637.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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 P 7 5.49 5 S 80 5.16 5 C 8822 2.51 5 N 2283 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13791 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "B" Number of atoms: 6035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6035 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 39, 'TRANS': 787} Chain breaks: 1 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'NAD': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13791 At special positions: 0 Unit cell: (140.58, 130.995, 132.06, 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) S 80 16.00 P 7 15.00 O 2599 8.00 N 2283 7.00 C 8822 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: 1.24 Conformation dependent library (CDL) restraints added in 655.8 milliseconds 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 10 sheets defined 57.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 removed outlier: 3.665A pdb=" N GLN A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.508A pdb=" N TYR A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.678A pdb=" N ALA A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.737A pdb=" N LEU A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.713A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.739A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 337 through 357 removed outlier: 4.053A pdb=" N SER A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.511A pdb=" N VAL A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.975A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 449 removed outlier: 3.969A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.935A pdb=" N SER A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 480 through 492 removed outlier: 3.705A pdb=" N SER A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.739A pdb=" N GLY A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 501 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 540 removed outlier: 3.731A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 removed outlier: 3.703A pdb=" N LEU A 554 " --> pdb=" O TYR A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 555 through 572 removed outlier: 4.176A pdb=" N ALA A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.757A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 624 removed outlier: 4.093A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 removed outlier: 3.610A pdb=" N LYS A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 682 removed outlier: 3.689A pdb=" N LEU A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 removed outlier: 3.541A pdb=" N PHE A 686 " --> pdb=" O TYR A 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 693 through 722 removed outlier: 4.005A pdb=" N ALA A 699 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.982A pdb=" N ALA A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 removed outlier: 4.123A pdb=" N VAL A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 796 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 837 removed outlier: 3.888A pdb=" N ILE A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 889 through 895 removed outlier: 4.338A pdb=" N CYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.816A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 938 removed outlier: 3.773A pdb=" N VAL A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 988 through 992 removed outlier: 3.789A pdb=" N SER A 992 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1015 removed outlier: 3.836A pdb=" N TYR A1015 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1042 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.768A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.926A pdb=" N TYR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.643A pdb=" N LEU B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.656A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 357 removed outlier: 3.799A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.789A pdb=" N VAL B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 449 removed outlier: 3.634A pdb=" N THR B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 removed outlier: 3.826A pdb=" N SER B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 481 through 492 removed outlier: 3.597A pdb=" N MET B 485 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.949A pdb=" N GLY B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 540 removed outlier: 3.700A pdb=" N SER B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 555 through 563 removed outlier: 4.442A pdb=" N ALA B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.801A pdb=" N ALA B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 Processing helix chain 'B' and resid 600 through 622 Processing helix chain 'B' and resid 626 through 650 removed outlier: 3.560A pdb=" N ALA B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.600A pdb=" N VAL B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 682 removed outlier: 4.041A pdb=" N GLY B 668 " --> pdb=" O HIS B 664 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 721 removed outlier: 4.895A pdb=" N ALA B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 748 through 753 Proline residue: B 751 - end of helix No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.759A pdb=" N GLY B 761 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 811 removed outlier: 3.827A pdb=" N THR B 793 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 837 removed outlier: 3.753A pdb=" N MET B 837 " --> pdb=" O MET B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.310A pdb=" N VAL A 16 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU A 49 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 18 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 46 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN A 71 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 48 " --> pdb=" O GLN A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.761A pdb=" N SER A 110 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.822A pdb=" N ILE A 96 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.007A pdb=" N LEU A 271 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA7, first strand: chain 'A' and resid 867 through 868 removed outlier: 7.046A pdb=" N THR A 867 " --> pdb=" O MET A1021 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 995 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 883 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 961 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 885 " --> pdb=" O LEU A 961 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE A 963 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A 887 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 884 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLY A 918 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 886 " --> pdb=" O GLY A 918 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LEU A 945 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 917 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 71 removed outlier: 7.185A pdb=" N VAL B 46 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN B 71 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 48 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 16 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU B 49 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 18 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 108 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 133 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 384 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 177 removed outlier: 3.883A pdb=" N THR B 177 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 180 " --> pdb=" O THR B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 210 removed outlier: 3.695A pdb=" N ILE B 270 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 271 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 325 " --> pdb=" O HIS B 322 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2058 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4230 1.34 - 1.46: 2730 1.46 - 1.58: 6938 1.58 - 1.70: 13 1.70 - 1.82: 142 Bond restraints: 14053 Sorted by residual: bond pdb=" O2B NAP A1101 " pdb=" P2B NAP A1101 " ideal model delta sigma weight residual 1.736 1.580 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3 NAD A1102 " pdb=" PA NAD A1102 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C THR B 546 " pdb=" N ASP B 547 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.00e+01 bond pdb=" O5D NAP A1101 " pdb=" PN NAP A1101 " ideal model delta sigma weight residual 1.649 1.590 0.059 2.00e-02 2.50e+03 8.72e+00 ... (remaining 14048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18267 2.36 - 4.72: 699 4.72 - 7.09: 112 7.09 - 9.45: 29 9.45 - 11.81: 3 Bond angle restraints: 19110 Sorted by residual: angle pdb=" N ALA A 518 " pdb=" CA ALA A 518 " pdb=" C ALA A 518 " ideal model delta sigma weight residual 113.18 103.98 9.20 1.33e+00 5.65e-01 4.78e+01 angle pdb=" C GLN B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 122.46 131.85 -9.39 1.41e+00 5.03e-01 4.43e+01 angle pdb=" C PHE B 371 " pdb=" N ASP B 372 " pdb=" CA ASP B 372 " ideal model delta sigma weight residual 122.44 114.57 7.87 1.19e+00 7.06e-01 4.38e+01 angle pdb=" C ALA A 38 " pdb=" N LEU A 39 " pdb=" CA LEU A 39 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ALA B 38 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 19105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 7878 16.23 - 32.46: 339 32.46 - 48.69: 76 48.69 - 64.92: 11 64.92 - 81.16: 14 Dihedral angle restraints: 8318 sinusoidal: 3087 harmonic: 5231 Sorted by residual: dihedral pdb=" CA LYS B 399 " pdb=" C LYS B 399 " pdb=" N ASN B 400 " pdb=" CA ASN B 400 " ideal model delta harmonic sigma weight residual -180.00 -138.96 -41.04 0 5.00e+00 4.00e-02 6.74e+01 dihedral pdb=" CA THR B 424 " pdb=" C THR B 424 " pdb=" N PRO B 425 " pdb=" CA PRO B 425 " ideal model delta harmonic sigma weight residual 180.00 -149.47 -30.53 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA GLN A 37 " pdb=" C GLN A 37 " pdb=" N ALA A 38 " pdb=" CA ALA A 38 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 8315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1647 0.059 - 0.119: 507 0.119 - 0.178: 102 0.178 - 0.238: 16 0.238 - 0.297: 3 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA TRP B 474 " pdb=" N TRP B 474 " pdb=" C TRP B 474 " pdb=" CB TRP B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA PHE B 365 " pdb=" N PHE B 365 " pdb=" C PHE B 365 " pdb=" CB PHE B 365 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE B 752 " pdb=" N PHE B 752 " pdb=" C PHE B 752 " pdb=" CB PHE B 752 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2272 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 18 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 19 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 752 " -0.025 2.00e-02 2.50e+03 2.19e-02 8.38e+00 pdb=" CG PHE B 752 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 752 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 752 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 752 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 752 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 752 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 673 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C LEU B 673 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 673 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 674 " -0.017 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2709 2.76 - 3.30: 13362 3.30 - 3.83: 22780 3.83 - 4.37: 26115 4.37 - 4.90: 44550 Nonbonded interactions: 109516 Sorted by model distance: nonbonded pdb=" O TYR B 566 " pdb=" OG SER B 569 " model vdw 2.230 3.040 nonbonded pdb=" O GLN B 340 " pdb=" OG1 THR B 343 " model vdw 2.267 3.040 nonbonded pdb=" O PHE A 954 " pdb=" OG SER A 992 " model vdw 2.275 3.040 nonbonded pdb=" O MET B 485 " pdb=" OG1 THR B 488 " model vdw 2.285 3.040 nonbonded pdb=" O GLY A 776 " pdb=" OG1 THR A 780 " model vdw 2.287 3.040 ... (remaining 109511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.830 Find NCS groups from input model: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.009 0.156 14053 Z= 0.392 Angle : 1.104 11.811 19110 Z= 0.599 Chirality : 0.059 0.297 2275 Planarity : 0.008 0.073 2416 Dihedral : 10.794 81.155 5010 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.16), residues: 1859 helix: -1.83 (0.13), residues: 985 sheet: -1.62 (0.41), residues: 147 loop : -3.04 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 734 TYR 0.027 0.003 TYR B 330 PHE 0.051 0.004 PHE B 752 TRP 0.025 0.004 TRP B 474 HIS 0.011 0.003 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.39 (14053) covalent geometry : angle 1.10439 / 0.60 (19110) hydrogen bonds : bond 0.18092 / 12.08 ( 702) hydrogen bonds : angle 7.27392 / 5.06 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8585 (tp30) cc_final: 0.8272 (tm-30) REVERT: A 60 ASP cc_start: 0.9161 (m-30) cc_final: 0.8822 (t70) REVERT: A 77 LEU cc_start: 0.9391 (mt) cc_final: 0.9079 (tp) REVERT: A 172 PHE cc_start: 0.9237 (m-10) cc_final: 0.8879 (m-10) REVERT: A 249 MET cc_start: 0.7611 (mmp) cc_final: 0.7355 (mmm) REVERT: A 286 PHE cc_start: 0.8659 (m-80) cc_final: 0.8230 (m-10) REVERT: A 288 LYS cc_start: 0.9299 (ptmm) cc_final: 0.9052 (ptpt) REVERT: A 296 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6704 (tm-30) REVERT: A 337 MET cc_start: 0.8594 (mtp) cc_final: 0.8386 (mtp) REVERT: A 345 TYR cc_start: 0.9065 (t80) cc_final: 0.8861 (t80) REVERT: A 414 GLU cc_start: 0.8046 (tt0) cc_final: 0.7824 (mt-10) REVERT: A 430 MET cc_start: 0.8947 (tpt) cc_final: 0.8674 (tpt) REVERT: A 458 MET cc_start: 0.9234 (tpp) cc_final: 0.8981 (tpp) REVERT: A 507 LEU cc_start: 0.8938 (mm) cc_final: 0.8694 (tt) REVERT: A 754 MET cc_start: 0.7578 (mpt) cc_final: 0.7048 (mmp) REVERT: A 764 CYS cc_start: 0.8918 (m) cc_final: 0.8631 (t) REVERT: A 869 ILE cc_start: 0.8925 (pt) cc_final: 0.8546 (pt) REVERT: A 873 ASN cc_start: 0.8463 (m110) cc_final: 0.7916 (t0) REVERT: A 877 MET cc_start: 0.9124 (ttp) cc_final: 0.8761 (ptm) REVERT: A 903 ASP cc_start: 0.8636 (t70) cc_final: 0.8237 (t0) REVERT: A 907 MET cc_start: 0.8713 (mtt) cc_final: 0.8294 (mmm) REVERT: A 947 MET cc_start: 0.9091 (ttp) cc_final: 0.8645 (tmm) REVERT: A 1021 MET cc_start: 0.8833 (mmm) cc_final: 0.8504 (mmm) REVERT: B 109 ILE cc_start: 0.8759 (mm) cc_final: 0.8323 (mm) REVERT: B 286 PHE cc_start: 0.8791 (m-80) cc_final: 0.8521 (m-80) REVERT: B 366 GLU cc_start: 0.8606 (tt0) cc_final: 0.8382 (tm-30) REVERT: B 458 MET cc_start: 0.8999 (tpp) cc_final: 0.8446 (tpp) REVERT: B 477 THR cc_start: 0.9384 (m) cc_final: 0.9174 (p) REVERT: B 538 MET cc_start: 0.8887 (mtp) cc_final: 0.8592 (mtp) REVERT: B 663 PHE cc_start: 0.8920 (m-10) cc_final: 0.8693 (m-10) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.1050 time to fit residues: 54.3137 Evaluate side-chains 182 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN A 310 ASN A 873 ASN A 931 ASN B 24 GLN B 62 HIS B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 527 ASN B 735 HIS B 796 ASN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 813 ASN B 838 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074195 restraints weight = 49818.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076101 restraints weight = 24509.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077345 restraints weight = 15142.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078151 restraints weight = 10974.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078620 restraints weight = 8870.293| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14053 Z= 0.203 Angle : 0.707 10.982 19110 Z= 0.359 Chirality : 0.045 0.221 2275 Planarity : 0.005 0.050 2416 Dihedral : 6.519 51.488 1993 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.14 % Allowed : 10.68 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1859 helix: 0.28 (0.16), residues: 1002 sheet: -1.38 (0.44), residues: 140 loop : -2.59 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 925 TYR 0.018 0.002 TYR B 330 PHE 0.037 0.002 PHE B 365 TRP 0.020 0.002 TRP A 801 HIS 0.008 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (14053) covalent geometry : angle 0.70726 / 0.36 (19110) hydrogen bonds : bond 0.05033 / 3.33 ( 702) hydrogen bonds : angle 4.56575 / 3.16 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8368 (tp30) cc_final: 0.8092 (tm-30) REVERT: A 288 LYS cc_start: 0.8848 (ptmm) cc_final: 0.8637 (mttp) REVERT: A 296 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6285 (tm-30) REVERT: A 325 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8770 (mp) REVERT: A 430 MET cc_start: 0.8267 (tpt) cc_final: 0.7742 (tpt) REVERT: A 754 MET cc_start: 0.6995 (mpt) cc_final: 0.6480 (mmp) REVERT: A 962 VAL cc_start: 0.9595 (t) cc_final: 0.9348 (p) REVERT: B 430 MET cc_start: 0.7694 (tmm) cc_final: 0.7489 (tmm) REVERT: B 458 MET cc_start: 0.8627 (tpp) cc_final: 0.8240 (tpp) REVERT: B 829 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8645 (tt) outliers start: 45 outliers final: 26 residues processed: 239 average time/residue: 0.0914 time to fit residues: 35.7133 Evaluate side-chains 174 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 838 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 10.0000 chunk 165 optimal weight: 0.2980 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 632 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 527 ASN B 796 ASN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075187 restraints weight = 50115.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077051 restraints weight = 24857.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078259 restraints weight = 15484.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079009 restraints weight = 11296.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079574 restraints weight = 9193.069| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14053 Z= 0.146 Angle : 0.644 9.185 19110 Z= 0.323 Chirality : 0.043 0.208 2275 Planarity : 0.005 0.045 2416 Dihedral : 5.942 47.657 1993 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 3.07 % Allowed : 13.34 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1859 helix: 1.09 (0.17), residues: 996 sheet: -1.17 (0.46), residues: 140 loop : -2.35 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1038 TYR 0.020 0.001 TYR B 551 PHE 0.031 0.002 PHE A 365 TRP 0.008 0.001 TRP A 801 HIS 0.007 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (14053) covalent geometry : angle 0.64416 / 0.32 (19110) hydrogen bonds : bond 0.04420 / 2.93 ( 702) hydrogen bonds : angle 4.22061 / 2.92 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8422 (tp30) cc_final: 0.8067 (tm-30) REVERT: A 288 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8632 (ptpp) REVERT: A 296 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6104 (tm-30) REVERT: A 430 MET cc_start: 0.8247 (tpt) cc_final: 0.7901 (ptt) REVERT: A 754 MET cc_start: 0.7003 (mpt) cc_final: 0.6458 (mmp) REVERT: A 947 MET cc_start: 0.8341 (tpp) cc_final: 0.7972 (tpp) REVERT: B 63 TYR cc_start: 0.8802 (m-80) cc_final: 0.8551 (m-80) REVERT: B 101 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 274 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 337 MET cc_start: 0.8572 (mtp) cc_final: 0.8124 (mmm) REVERT: B 458 MET cc_start: 0.8644 (tpp) cc_final: 0.8200 (tpp) REVERT: B 524 SER cc_start: 0.8181 (p) cc_final: 0.7964 (m) REVERT: B 592 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 737 LEU cc_start: 0.8300 (tp) cc_final: 0.8001 (tp) REVERT: B 742 LEU cc_start: 0.8026 (mt) cc_final: 0.7753 (mt) REVERT: B 829 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8634 (tt) outliers start: 44 outliers final: 26 residues processed: 208 average time/residue: 0.0870 time to fit residues: 29.7838 Evaluate side-chains 183 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 135 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 866 HIS B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073955 restraints weight = 49534.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075892 restraints weight = 23798.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077162 restraints weight = 14556.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077981 restraints weight = 10492.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078409 restraints weight = 8454.343| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14053 Z= 0.135 Angle : 0.615 8.777 19110 Z= 0.306 Chirality : 0.042 0.212 2275 Planarity : 0.004 0.045 2416 Dihedral : 5.534 50.399 1993 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.63 % Allowed : 13.62 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1859 helix: 1.57 (0.17), residues: 999 sheet: -0.98 (0.47), residues: 136 loop : -2.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 925 TYR 0.023 0.001 TYR B 551 PHE 0.032 0.002 PHE A 365 TRP 0.008 0.001 TRP B 801 HIS 0.006 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14053) covalent geometry : angle 0.61469 / 0.31 (19110) hydrogen bonds : bond 0.04057 / 2.69 ( 702) hydrogen bonds : angle 3.96755 / 2.75 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8460 (tp30) cc_final: 0.8041 (tm-30) REVERT: A 288 LYS cc_start: 0.8968 (ptmm) cc_final: 0.8667 (ptpp) REVERT: A 296 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6173 (tm-30) REVERT: A 393 PHE cc_start: 0.7582 (t80) cc_final: 0.7369 (t80) REVERT: A 430 MET cc_start: 0.8233 (tpt) cc_final: 0.7799 (ptt) REVERT: A 633 MET cc_start: 0.8466 (mtm) cc_final: 0.8199 (mtm) REVERT: A 754 MET cc_start: 0.6958 (mpt) cc_final: 0.6434 (mmp) REVERT: A 947 MET cc_start: 0.8419 (tpp) cc_final: 0.8119 (tpp) REVERT: B 28 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8287 (ptt90) REVERT: B 63 TYR cc_start: 0.8806 (m-80) cc_final: 0.8595 (m-80) REVERT: B 430 MET cc_start: 0.7605 (tmm) cc_final: 0.7397 (tmm) REVERT: B 458 MET cc_start: 0.8680 (tpp) cc_final: 0.8137 (tpp) REVERT: B 829 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8587 (tt) outliers start: 52 outliers final: 24 residues processed: 218 average time/residue: 0.0879 time to fit residues: 31.5964 Evaluate side-chains 182 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072327 restraints weight = 50484.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074221 restraints weight = 23846.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075434 restraints weight = 14634.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076247 restraints weight = 10627.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076740 restraints weight = 8577.837| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14053 Z= 0.180 Angle : 0.663 12.178 19110 Z= 0.327 Chirality : 0.043 0.181 2275 Planarity : 0.004 0.042 2416 Dihedral : 5.549 56.167 1993 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer: Outliers : 3.56 % Allowed : 14.87 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1859 helix: 1.75 (0.17), residues: 1003 sheet: -0.87 (0.48), residues: 136 loop : -2.14 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 734 TYR 0.019 0.001 TYR A 555 PHE 0.026 0.002 PHE A 365 TRP 0.007 0.001 TRP B 801 HIS 0.006 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (14053) covalent geometry : angle 0.66258 / 0.33 (19110) hydrogen bonds : bond 0.04312 / 2.86 ( 702) hydrogen bonds : angle 4.04962 / 2.81 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8541 (tp30) cc_final: 0.8033 (tm-30) REVERT: A 288 LYS cc_start: 0.8981 (ptmm) cc_final: 0.8677 (ptpp) REVERT: A 296 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6172 (tm-30) REVERT: A 319 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 430 MET cc_start: 0.8243 (tpt) cc_final: 0.7813 (ptt) REVERT: A 633 MET cc_start: 0.8530 (mtm) cc_final: 0.8248 (mtm) REVERT: A 742 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 754 MET cc_start: 0.7017 (mpt) cc_final: 0.6377 (mmp) REVERT: A 947 MET cc_start: 0.8436 (tpp) cc_final: 0.8230 (tpp) REVERT: A 984 MET cc_start: 0.8077 (tpp) cc_final: 0.7830 (tpp) REVERT: B 28 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8323 (ptt90) REVERT: B 63 TYR cc_start: 0.8756 (m-80) cc_final: 0.8519 (m-80) REVERT: B 274 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.8995 (p) REVERT: B 337 MET cc_start: 0.8848 (mtp) cc_final: 0.8353 (ttm) REVERT: B 430 MET cc_start: 0.7692 (tmm) cc_final: 0.7452 (tmm) REVERT: B 458 MET cc_start: 0.8731 (tpp) cc_final: 0.8284 (tpp) REVERT: B 538 MET cc_start: 0.8203 (ttp) cc_final: 0.7921 (ttp) REVERT: B 592 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8903 (mm) REVERT: B 829 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8517 (tt) outliers start: 51 outliers final: 29 residues processed: 195 average time/residue: 0.0892 time to fit residues: 28.5093 Evaluate side-chains 182 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 ASN A 931 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.086229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071797 restraints weight = 49531.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073678 restraints weight = 23772.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074914 restraints weight = 14519.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075712 restraints weight = 10496.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076222 restraints weight = 8481.989| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14053 Z= 0.191 Angle : 0.671 11.413 19110 Z= 0.331 Chirality : 0.044 0.290 2275 Planarity : 0.004 0.038 2416 Dihedral : 5.531 55.308 1993 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.84 % Allowed : 15.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1859 helix: 1.87 (0.17), residues: 1001 sheet: -1.01 (0.46), residues: 140 loop : -2.09 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 734 TYR 0.020 0.001 TYR B 551 PHE 0.025 0.002 PHE A 393 TRP 0.008 0.001 TRP B 801 HIS 0.006 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (14053) covalent geometry : angle 0.67141 / 0.33 (19110) hydrogen bonds : bond 0.04406 / 2.92 ( 702) hydrogen bonds : angle 4.07420 / 2.82 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8579 (tp30) cc_final: 0.8090 (tm-30) REVERT: A 288 LYS cc_start: 0.9044 (ptmm) cc_final: 0.8737 (ptpp) REVERT: A 296 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6247 (tm-30) REVERT: A 319 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7185 (tp) REVERT: A 430 MET cc_start: 0.8219 (tpt) cc_final: 0.7790 (ptt) REVERT: A 580 MET cc_start: 0.8670 (mmm) cc_final: 0.8450 (tpt) REVERT: A 633 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: A 742 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8121 (tt) REVERT: A 754 MET cc_start: 0.6594 (mpt) cc_final: 0.6092 (mmp) REVERT: A 833 MET cc_start: 0.8472 (ttt) cc_final: 0.8270 (ttt) REVERT: B 28 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8301 (ptt90) REVERT: B 274 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 337 MET cc_start: 0.8882 (mtp) cc_final: 0.8413 (ttm) REVERT: B 458 MET cc_start: 0.8768 (tpp) cc_final: 0.8317 (tpp) REVERT: B 485 MET cc_start: 0.8140 (mmt) cc_final: 0.7882 (mmt) REVERT: B 538 MET cc_start: 0.8244 (ttp) cc_final: 0.7924 (ttp) REVERT: B 592 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 829 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8530 (tt) outliers start: 55 outliers final: 36 residues processed: 198 average time/residue: 0.0918 time to fit residues: 29.7417 Evaluate side-chains 192 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 chunk 71 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073416 restraints weight = 49368.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075305 restraints weight = 23429.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076542 restraints weight = 14338.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077353 restraints weight = 10356.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077834 restraints weight = 8348.694| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14053 Z= 0.133 Angle : 0.639 10.637 19110 Z= 0.310 Chirality : 0.043 0.344 2275 Planarity : 0.004 0.037 2416 Dihedral : 5.330 58.854 1993 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.49 % Allowed : 15.99 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1859 helix: 2.07 (0.17), residues: 1001 sheet: -0.79 (0.47), residues: 138 loop : -2.00 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.014 0.001 TYR B 551 PHE 0.019 0.001 PHE A 365 TRP 0.008 0.001 TRP B 801 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14053) covalent geometry : angle 0.63889 / 0.31 (19110) hydrogen bonds : bond 0.03960 / 2.63 ( 702) hydrogen bonds : angle 3.90104 / 2.70 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9023 (ptmm) cc_final: 0.8796 (ptpp) REVERT: A 296 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6120 (tm-30) REVERT: A 430 MET cc_start: 0.8193 (tpt) cc_final: 0.7755 (ptt) REVERT: A 633 MET cc_start: 0.8581 (mtm) cc_final: 0.8203 (mtm) REVERT: A 742 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8035 (tt) REVERT: A 754 MET cc_start: 0.6549 (mpt) cc_final: 0.5995 (mmp) REVERT: A 947 MET cc_start: 0.8531 (tpp) cc_final: 0.8253 (tpp) REVERT: B 28 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8304 (ptt90) REVERT: B 63 TYR cc_start: 0.8699 (m-10) cc_final: 0.8338 (m-80) REVERT: B 274 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.8951 (p) REVERT: B 345 TYR cc_start: 0.8617 (t80) cc_final: 0.8302 (t80) REVERT: B 458 MET cc_start: 0.8729 (tpp) cc_final: 0.8293 (tpp) REVERT: B 538 MET cc_start: 0.8144 (ttp) cc_final: 0.7844 (ttp) REVERT: B 592 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8869 (mm) outliers start: 50 outliers final: 33 residues processed: 205 average time/residue: 0.0924 time to fit residues: 30.6961 Evaluate side-chains 191 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 152 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN B 527 ASN B 552 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075050 restraints weight = 49219.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076942 restraints weight = 23479.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078188 restraints weight = 14389.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078993 restraints weight = 10376.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079453 restraints weight = 8383.010| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14053 Z= 0.115 Angle : 0.629 10.993 19110 Z= 0.305 Chirality : 0.043 0.359 2275 Planarity : 0.004 0.038 2416 Dihedral : 5.143 59.886 1993 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.72 % Allowed : 16.90 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1859 helix: 2.21 (0.17), residues: 1000 sheet: -0.71 (0.46), residues: 138 loop : -1.89 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 925 TYR 0.009 0.001 TYR A 683 PHE 0.027 0.001 PHE A 393 TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14053) covalent geometry : angle 0.62889 / 0.30 (19110) hydrogen bonds : bond 0.03698 / 2.44 ( 702) hydrogen bonds : angle 3.77600 / 2.62 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8815 (ptpp) REVERT: A 296 GLU cc_start: 0.6510 (mm-30) cc_final: 0.6070 (tm-30) REVERT: A 319 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6940 (tp) REVERT: A 430 MET cc_start: 0.8075 (tpt) cc_final: 0.7699 (ptt) REVERT: A 485 MET cc_start: 0.8775 (mmm) cc_final: 0.8567 (mmm) REVERT: A 633 MET cc_start: 0.8486 (mtm) cc_final: 0.8265 (mtm) REVERT: A 742 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 754 MET cc_start: 0.6619 (mpt) cc_final: 0.6049 (mmp) REVERT: A 798 TYR cc_start: 0.8955 (m-80) cc_final: 0.8694 (m-80) REVERT: A 947 MET cc_start: 0.8493 (tpp) cc_final: 0.8218 (tpp) REVERT: B 28 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8459 (ptt180) REVERT: B 63 TYR cc_start: 0.8661 (m-10) cc_final: 0.8278 (m-80) REVERT: B 274 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.8993 (p) REVERT: B 458 MET cc_start: 0.8675 (tpp) cc_final: 0.8248 (tpp) REVERT: B 503 MET cc_start: 0.6120 (mtm) cc_final: 0.5157 (ptp) REVERT: B 592 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 714 LEU cc_start: 0.7791 (tp) cc_final: 0.7492 (pp) outliers start: 39 outliers final: 26 residues processed: 200 average time/residue: 0.0963 time to fit residues: 31.3415 Evaluate side-chains 185 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073981 restraints weight = 49590.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075905 restraints weight = 23768.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077141 restraints weight = 14501.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077944 restraints weight = 10462.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078448 restraints weight = 8454.198| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14053 Z= 0.143 Angle : 0.672 11.514 19110 Z= 0.322 Chirality : 0.044 0.381 2275 Planarity : 0.004 0.037 2416 Dihedral : 5.108 59.481 1993 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.93 % Allowed : 17.67 % Favored : 79.40 % 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 are not related in a simple way. whole: 0.68 (0.21), residues: 1859 helix: 2.13 (0.17), residues: 1001 sheet: -0.64 (0.47), residues: 138 loop : -1.88 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 427 TYR 0.011 0.001 TYR B 364 PHE 0.017 0.001 PHE B 752 TRP 0.007 0.001 TRP B 801 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14053) covalent geometry : angle 0.67232 / 0.32 (19110) hydrogen bonds : bond 0.03881 / 2.57 ( 702) hydrogen bonds : angle 3.86739 / 2.67 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.9043 (tpp) cc_final: 0.8656 (tpt) REVERT: A 288 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8722 (ptpp) REVERT: A 296 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6101 (tm-30) REVERT: A 319 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6989 (tp) REVERT: A 430 MET cc_start: 0.8114 (tpt) cc_final: 0.7729 (ptt) REVERT: A 485 MET cc_start: 0.8777 (mmm) cc_final: 0.8546 (mmm) REVERT: A 580 MET cc_start: 0.8586 (mmm) cc_final: 0.8373 (tpt) REVERT: A 742 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7976 (tt) REVERT: A 754 MET cc_start: 0.6568 (mpt) cc_final: 0.6003 (mmp) REVERT: A 798 TYR cc_start: 0.8961 (m-80) cc_final: 0.8700 (m-80) REVERT: A 947 MET cc_start: 0.8518 (tpp) cc_final: 0.8235 (tpp) REVERT: B 28 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8299 (ptt90) REVERT: B 63 TYR cc_start: 0.8701 (m-10) cc_final: 0.8337 (m-80) REVERT: B 274 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9013 (p) REVERT: B 345 TYR cc_start: 0.8616 (t80) cc_final: 0.7766 (t80) REVERT: B 458 MET cc_start: 0.8692 (tpp) cc_final: 0.8274 (tpp) REVERT: B 592 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 829 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8610 (tt) outliers start: 42 outliers final: 33 residues processed: 187 average time/residue: 0.0882 time to fit residues: 27.2093 Evaluate side-chains 193 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 474 TRP Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 158 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 131 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 6 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075182 restraints weight = 49029.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077112 restraints weight = 23748.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078367 restraints weight = 14547.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079183 restraints weight = 10504.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079619 restraints weight = 8475.906| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14053 Z= 0.120 Angle : 0.666 11.585 19110 Z= 0.317 Chirality : 0.044 0.386 2275 Planarity : 0.004 0.037 2416 Dihedral : 4.961 56.899 1993 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.72 % Allowed : 18.02 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1859 helix: 2.22 (0.17), residues: 994 sheet: -0.60 (0.47), residues: 138 loop : -1.83 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 734 TYR 0.012 0.001 TYR B 345 PHE 0.015 0.001 PHE B 752 TRP 0.007 0.001 TRP B 474 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14053) covalent geometry : angle 0.66569 / 0.32 (19110) hydrogen bonds : bond 0.03687 / 2.46 ( 702) hydrogen bonds : angle 3.79269 / 2.62 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3718 Ramachandran restraints generated. 1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9017 (ptmm) cc_final: 0.8762 (ptpp) REVERT: A 296 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6103 (tm-30) REVERT: A 319 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6835 (tp) REVERT: A 430 MET cc_start: 0.8100 (tpt) cc_final: 0.7710 (ptt) REVERT: A 485 MET cc_start: 0.8763 (mmm) cc_final: 0.8501 (mmm) REVERT: A 742 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 754 MET cc_start: 0.6528 (mpt) cc_final: 0.5922 (mmp) REVERT: A 798 TYR cc_start: 0.8939 (m-80) cc_final: 0.8684 (m-80) REVERT: A 890 TYR cc_start: 0.7545 (t80) cc_final: 0.7334 (t80) REVERT: A 947 MET cc_start: 0.8498 (tpp) cc_final: 0.8223 (tpp) REVERT: B 28 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8435 (ptt180) REVERT: B 63 TYR cc_start: 0.8693 (m-10) cc_final: 0.8319 (m-80) REVERT: B 274 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9031 (p) REVERT: B 458 MET cc_start: 0.8663 (tpp) cc_final: 0.8270 (tpp) REVERT: B 592 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8841 (mm) REVERT: B 714 LEU cc_start: 0.7788 (tp) cc_final: 0.7486 (pp) outliers start: 39 outliers final: 28 residues processed: 194 average time/residue: 0.0888 time to fit residues: 28.3836 Evaluate side-chains 189 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072968 restraints weight = 50774.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074818 restraints weight = 24777.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076049 restraints weight = 15346.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076842 restraints weight = 11181.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077270 restraints weight = 9083.046| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14053 Z= 0.171 Angle : 0.703 16.009 19110 Z= 0.338 Chirality : 0.045 0.366 2275 Planarity : 0.004 0.036 2416 Dihedral : 5.038 56.192 1993 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.72 % Allowed : 18.51 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1859 helix: 2.17 (0.17), residues: 995 sheet: -0.64 (0.46), residues: 138 loop : -1.85 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 734 TYR 0.017 0.001 TYR B 345 PHE 0.026 0.002 PHE A 393 TRP 0.009 0.002 TRP B 801 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (14053) covalent geometry : angle 0.70322 / 0.34 (19110) hydrogen bonds : bond 0.04138 / 2.76 ( 702) hydrogen bonds : angle 3.93807 / 2.72 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.88 seconds wall clock time: 40 minutes 0.32 seconds (2400.32 seconds total)