Starting phenix.real_space_refine on Sat Aug 23 18:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6que_4637/08_2025/6que_4637.cif Found real_map, /net/cci-nas-00/data/ceres_data/6que_4637/08_2025/6que_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_4637/08_2025/6que_4637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6que_4637/08_2025/6que_4637.map" model { file = "/net/cci-nas-00/data/ceres_data/6que_4637/08_2025/6que_4637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6que_4637/08_2025/6que_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-2.0-5787/lib/python3.9/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: 2.94, per 1000 atoms: 0.21 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: 0.86 Conformation dependent library (CDL) restraints added in 605.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.19 Time building geometry restraints manager: 1.23 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: 7937 16.23 - 32.46: 382 32.46 - 48.69: 87 48.69 - 64.92: 35 64.92 - 81.16: 23 Dihedral angle restraints: 8464 sinusoidal: 3233 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 8461 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 12.099 81.155 5156 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 aren 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 covalent geometry : bond 0.00871 (14053) covalent geometry : angle 1.10439 (19110) hydrogen bonds : bond 0.18092 ( 702) hydrogen bonds : angle 7.27392 ( 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 : 0.336 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: 0.0867 time to fit residues: 44.6276 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 : 0.519 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 310 ASN A 873 ASN A 931 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074180 restraints weight = 49739.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076023 restraints weight = 24630.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077257 restraints weight = 15372.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078064 restraints weight = 11144.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078563 restraints weight = 8976.489| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14053 Z= 0.207 Angle : 0.719 11.258 19110 Z= 0.364 Chirality : 0.045 0.249 2275 Planarity : 0.005 0.050 2416 Dihedral : 8.921 51.243 2139 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.14 % Allowed : 10.61 % Favored : 86.24 % 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 aren not related in a simple way. whole: -1.46 (0.19), residues: 1859 helix: 0.21 (0.16), residues: 1000 sheet: -1.52 (0.42), residues: 149 loop : -2.58 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 925 TYR 0.017 0.002 TYR B 330 PHE 0.035 0.002 PHE B 365 TRP 0.018 0.002 TRP A 801 HIS 0.007 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00467 (14053) covalent geometry : angle 0.71880 (19110) hydrogen bonds : bond 0.05265 ( 702) hydrogen bonds : angle 4.66809 ( 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 246 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8339 (tp30) cc_final: 0.8122 (tm-30) REVERT: A 296 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6261 (tm-30) REVERT: A 325 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 430 MET cc_start: 0.8209 (tpt) cc_final: 0.7692 (tpt) REVERT: A 754 MET cc_start: 0.6985 (mpt) cc_final: 0.6485 (mmp) REVERT: A 962 VAL cc_start: 0.9586 (t) cc_final: 0.9357 (p) REVERT: B 206 MET cc_start: 0.7931 (ttm) cc_final: 0.7702 (ttm) REVERT: B 345 TYR cc_start: 0.8796 (t80) cc_final: 0.8317 (t80) REVERT: B 458 MET cc_start: 0.8613 (tpp) cc_final: 0.8238 (tpp) REVERT: B 829 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8678 (tt) outliers start: 45 outliers final: 26 residues processed: 236 average time/residue: 0.0745 time to fit residues: 28.5822 Evaluate side-chains 176 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 939 VAL 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 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: 8.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN B 24 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 796 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.086994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072561 restraints weight = 50183.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074482 restraints weight = 24036.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075726 restraints weight = 14767.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076455 restraints weight = 10664.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077041 restraints weight = 8743.314| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.004 0.042 14053 Z= 0.188 Angle : 0.685 10.568 19110 Z= 0.343 Chirality : 0.044 0.212 2275 Planarity : 0.005 0.047 2416 Dihedral : 7.654 56.606 2139 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 3.28 % Allowed : 13.13 % 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 aren not related in a simple way. whole: -0.63 (0.20), residues: 1859 helix: 1.01 (0.17), residues: 998 sheet: -1.18 (0.47), residues: 140 loop : -2.38 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 734 TYR 0.020 0.002 TYR B 551 PHE 0.031 0.002 PHE A 365 TRP 0.011 0.002 TRP A 801 HIS 0.007 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00427 (14053) covalent geometry : angle 0.68477 (19110) hydrogen bonds : bond 0.04694 ( 702) hydrogen bonds : angle 4.32571 ( 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 214 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8464 (tp30) cc_final: 0.8111 (tm-30) REVERT: A 296 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6239 (tm-30) REVERT: A 325 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 430 MET cc_start: 0.8256 (tpt) cc_final: 0.7758 (tpt) REVERT: A 633 MET cc_start: 0.8434 (mtm) cc_final: 0.8103 (mtm) REVERT: A 742 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 754 MET cc_start: 0.7012 (mpt) cc_final: 0.6463 (mmp) REVERT: A 962 VAL cc_start: 0.9596 (t) cc_final: 0.9342 (p) REVERT: A 1021 MET cc_start: 0.8672 (mmt) cc_final: 0.8438 (mmm) REVERT: B 63 TYR cc_start: 0.8838 (m-80) cc_final: 0.8587 (m-80) REVERT: B 101 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (tt) REVERT: B 337 MET cc_start: 0.8781 (mtp) cc_final: 0.8414 (mtp) REVERT: B 345 TYR cc_start: 0.8735 (t80) cc_final: 0.8450 (t80) REVERT: B 458 MET cc_start: 0.8672 (tpp) cc_final: 0.8229 (tpp) REVERT: B 524 SER cc_start: 0.8252 (p) cc_final: 0.8051 (m) REVERT: B 592 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 737 LEU cc_start: 0.8324 (tp) cc_final: 0.8041 (tp) REVERT: B 829 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 47 outliers final: 28 residues processed: 204 average time/residue: 0.0721 time to fit residues: 24.2087 Evaluate side-chains 178 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 14 LEU 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 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 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 709 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 165 optimal weight: 0.0570 chunk 134 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 49 optimal weight: 0.0870 chunk 9 optimal weight: 7.9990 overall best weight: 2.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 HIS B 166 ASN B 310 ASN B 527 ASN B 812 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074894 restraints weight = 48687.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076810 restraints weight = 22851.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078083 restraints weight = 13979.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078922 restraints weight = 10061.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079465 restraints weight = 8072.731| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14053 Z= 0.118 Angle : 0.606 8.561 19110 Z= 0.300 Chirality : 0.042 0.207 2275 Planarity : 0.004 0.044 2416 Dihedral : 6.901 57.308 2139 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.49 % Allowed : 13.62 % Favored : 82.89 % 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 aren not related in a simple way. whole: -0.04 (0.21), residues: 1859 helix: 1.59 (0.17), residues: 995 sheet: -0.95 (0.47), residues: 136 loop : -2.26 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.020 0.001 TYR B 551 PHE 0.031 0.001 PHE A 365 TRP 0.007 0.001 TRP B 801 HIS 0.006 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00261 (14053) covalent geometry : angle 0.60632 (19110) hydrogen bonds : bond 0.03933 ( 702) hydrogen bonds : angle 3.97136 ( 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 237 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8446 (tp30) cc_final: 0.8014 (tm-30) REVERT: A 296 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6066 (tm-30) REVERT: A 430 MET cc_start: 0.8187 (tpt) cc_final: 0.7781 (ptt) REVERT: A 633 MET cc_start: 0.8447 (mtm) cc_final: 0.8166 (mtm) REVERT: A 754 MET cc_start: 0.7002 (mpt) cc_final: 0.6459 (mmp) REVERT: B 28 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8319 (ptt90) REVERT: B 249 MET cc_start: 0.8138 (mmm) cc_final: 0.7903 (mmm) REVERT: B 274 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 337 MET cc_start: 0.8699 (mtp) cc_final: 0.8441 (mtp) REVERT: B 345 TYR cc_start: 0.8534 (t80) cc_final: 0.8217 (t80) REVERT: B 458 MET cc_start: 0.8630 (tpp) cc_final: 0.8053 (tpp) REVERT: B 737 LEU cc_start: 0.8399 (tp) cc_final: 0.8188 (tp) REVERT: B 750 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8203 (pp) outliers start: 50 outliers final: 22 residues processed: 223 average time/residue: 0.0756 time to fit residues: 27.6945 Evaluate side-chains 175 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 962 VAL 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 155 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 526 VAL Chi-restraints excluded: chain B residue 626 CYS Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 750 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.798 > 50: distance: 22 - 27: 34.235 distance: 27 - 28: 43.699 distance: 28 - 29: 43.555 distance: 28 - 31: 45.763 distance: 29 - 30: 47.072 distance: 31 - 32: 41.173 distance: 32 - 33: 40.421 distance: 32 - 34: 39.410 distance: 36 - 37: 11.770 distance: 36 - 39: 41.968 distance: 37 - 38: 57.739 distance: 37 - 44: 12.653 distance: 39 - 40: 11.140 distance: 41 - 42: 40.395 distance: 42 - 43: 68.770 distance: 45 - 48: 40.175 distance: 46 - 47: 56.291 distance: 46 - 50: 37.400 distance: 48 - 49: 40.029 distance: 51 - 52: 40.515 distance: 51 - 54: 55.514 distance: 52 - 53: 38.913 distance: 52 - 55: 11.605 distance: 55 - 56: 9.236 distance: 55 - 61: 40.916 distance: 56 - 59: 40.837 distance: 57 - 58: 40.796 distance: 57 - 62: 41.437 distance: 59 - 60: 40.160 distance: 60 - 61: 40.289 distance: 62 - 63: 33.636 distance: 67 - 68: 40.155 distance: 67 - 69: 39.108 distance: 70 - 71: 41.047 distance: 71 - 72: 40.059 distance: 72 - 78: 55.458 distance: 75 - 76: 40.535 distance: 75 - 77: 40.979 distance: 78 - 79: 40.119 distance: 79 - 82: 56.947 distance: 80 - 81: 39.277 distance: 82 - 83: 38.591 distance: 83 - 84: 70.231 distance: 83 - 85: 56.400 distance: 86 - 87: 38.854 distance: 86 - 92: 57.744 distance: 87 - 88: 41.532 distance: 87 - 90: 39.758 distance: 88 - 89: 55.083 distance: 90 - 91: 57.092 distance: 93 - 94: 55.710 distance: 95 - 97: 34.728