Starting phenix.real_space_refine on Tue Aug 26 15:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhn_19177/08_2025/8rhn_19177.cif" } resolution = 4.5 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= 0.004 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 173 5.16 5 C 24353 2.51 5 N 6724 2.21 5 O 7118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.04s 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: 38368 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4056 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 32, 'TRANS': 493} Chain: "L" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4226 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 32, 'TRANS': 512} Chain: "M" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4056 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 32, 'TRANS': 493} Chain: "N" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4228 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 513} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4016 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 33, 'TRANS': 493} Chain breaks: 2 Chain: "P" Number of atoms: 4027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4027 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 33, 'TRANS': 495} Chain breaks: 2 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1585 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "C" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1211 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 2 Chain: "D" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1258 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "E" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1392 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1346 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1379 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 1 Chain: "H" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1358 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "I" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1320 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 21, 'TRANS': 161} Chain: "J" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 21, 'TRANS': 159} Time building chain proxies: 7.81, per 1000 atoms: 0.20 Number of scatterers: 38368 At special positions: 0 Unit cell: (148, 143.56, 160.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 173 16.00 O 7118 8.00 N 6724 7.00 C 24353 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9250 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 35 sheets defined 53.2% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'K' and resid 358 through 375 Proline residue: K 372 - end of helix Processing helix chain 'K' and resid 375 through 382 removed outlier: 3.733A pdb=" N PHE K 379 " --> pdb=" O GLN K 375 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 410 Processing helix chain 'K' and resid 421 through 424 Processing helix chain 'K' and resid 429 through 445 Processing helix chain 'K' and resid 454 through 459 removed outlier: 3.509A pdb=" N LEU K 458 " --> pdb=" O GLU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 488 removed outlier: 3.793A pdb=" N LYS K 471 " --> pdb=" O ASN K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 510 Processing helix chain 'K' and resid 525 through 537 Processing helix chain 'K' and resid 538 through 540 No H-bonds generated for 'chain 'K' and resid 538 through 540' Processing helix chain 'K' and resid 545 through 555 Processing helix chain 'K' and resid 560 through 581 Processing helix chain 'K' and resid 598 through 609 removed outlier: 3.753A pdb=" N PHE K 602 " --> pdb=" O THR K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 649 Proline residue: K 646 - end of helix Processing helix chain 'K' and resid 649 through 656 Processing helix chain 'K' and resid 673 through 686 removed outlier: 3.522A pdb=" N GLY K 686 " --> pdb=" O ALA K 682 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 698 Processing helix chain 'K' and resid 703 through 719 Processing helix chain 'K' and resid 728 through 732 Processing helix chain 'K' and resid 743 through 758 Processing helix chain 'K' and resid 779 through 784 Processing helix chain 'K' and resid 798 through 813 Processing helix chain 'K' and resid 820 through 829 removed outlier: 4.129A pdb=" N LEU K 824 " --> pdb=" O ASP K 820 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP K 829 " --> pdb=" O ILE K 825 " (cutoff:3.500A) Processing helix chain 'K' and resid 832 through 851 Processing helix chain 'K' and resid 858 through 869 removed outlier: 3.887A pdb=" N PHE K 862 " --> pdb=" O MET K 858 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 375 removed outlier: 3.909A pdb=" N LEU L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Proline residue: L 372 - end of helix Processing helix chain 'L' and resid 375 through 383 removed outlier: 3.631A pdb=" N PHE L 379 " --> pdb=" O GLN L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 409 Processing helix chain 'L' and resid 419 through 424 Processing helix chain 'L' and resid 429 through 445 Processing helix chain 'L' and resid 454 through 459 Processing helix chain 'L' and resid 467 through 483 removed outlier: 3.554A pdb=" N LYS L 471 " --> pdb=" O ASN L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 506 through 511 Processing helix chain 'L' and resid 525 through 538 Processing helix chain 'L' and resid 545 through 556 Processing helix chain 'L' and resid 560 through 581 Processing helix chain 'L' and resid 587 through 595 Processing helix chain 'L' and resid 598 through 609 Processing helix chain 'L' and resid 625 through 629 Processing helix chain 'L' and resid 632 through 645 Processing helix chain 'L' and resid 648 through 656 Processing helix chain 'L' and resid 673 through 686 Processing helix chain 'L' and resid 694 through 698 Processing helix chain 'L' and resid 703 through 719 Processing helix chain 'L' and resid 742 through 758 removed outlier: 3.811A pdb=" N ALA L 746 " --> pdb=" O ALA L 742 " (cutoff:3.500A) Processing helix chain 'L' and resid 774 through 778 Processing helix chain 'L' and resid 779 through 784 removed outlier: 3.720A pdb=" N MET L 783 " --> pdb=" O ASP L 779 " (cutoff:3.500A) Processing helix chain 'L' and resid 798 through 811 Processing helix chain 'L' and resid 820 through 827 removed outlier: 3.502A pdb=" N LEU L 824 " --> pdb=" O ASP L 820 " (cutoff:3.500A) Processing helix chain 'L' and resid 832 through 851 Processing helix chain 'L' and resid 858 through 869 Processing helix chain 'L' and resid 874 through 887 removed outlier: 3.934A pdb=" N ARG L 878 " --> pdb=" O PRO L 874 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 Proline residue: M 372 - end of helix Processing helix chain 'M' and resid 375 through 382 removed outlier: 4.105A pdb=" N PHE M 379 " --> pdb=" O GLN M 375 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR M 382 " --> pdb=" O LEU M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 411 Processing helix chain 'M' and resid 420 through 424 Processing helix chain 'M' and resid 429 through 445 Processing helix chain 'M' and resid 454 through 459 removed outlier: 4.131A pdb=" N LEU M 458 " --> pdb=" O GLU M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 484 removed outlier: 4.120A pdb=" N LYS M 471 " --> pdb=" O ASN M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 538 Processing helix chain 'M' and resid 545 through 555 Processing helix chain 'M' and resid 560 through 583 removed outlier: 3.504A pdb=" N GLN M 583 " --> pdb=" O ILE M 579 " (cutoff:3.500A) Processing helix chain 'M' and resid 587 through 591 Processing helix chain 'M' and resid 598 through 608 removed outlier: 3.724A pdb=" N PHE M 602 " --> pdb=" O THR M 598 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP M 608 " --> pdb=" O GLN M 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 625 through 629 Processing helix chain 'M' and resid 632 through 653 Proline residue: M 646 - end of helix Proline residue: M 650 - end of helix Processing helix chain 'M' and resid 654 through 657 Processing helix chain 'M' and resid 673 through 686 removed outlier: 3.589A pdb=" N GLY M 686 " --> pdb=" O ALA M 682 " (cutoff:3.500A) Processing helix chain 'M' and resid 694 through 698 Processing helix chain 'M' and resid 703 through 719 Processing helix chain 'M' and resid 728 through 732 Processing helix chain 'M' and resid 742 through 758 removed outlier: 3.692A pdb=" N ALA M 746 " --> pdb=" O ALA M 742 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG M 748 " --> pdb=" O ASN M 744 " (cutoff:3.500A) Processing helix chain 'M' and resid 774 through 778 Processing helix chain 'M' and resid 779 through 784 Processing helix chain 'M' and resid 798 through 813 Processing helix chain 'M' and resid 820 through 828 removed outlier: 4.033A pdb=" N LEU M 824 " --> pdb=" O ASP M 820 " (cutoff:3.500A) Processing helix chain 'M' and resid 832 through 851 Processing helix chain 'M' and resid 858 through 869 Processing helix chain 'N' and resid 351 through 355 Processing helix chain 'N' and resid 358 through 375 removed outlier: 4.133A pdb=" N LEU N 371 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Proline residue: N 372 - end of helix Processing helix chain 'N' and resid 375 through 381 Processing helix chain 'N' and resid 400 through 412 Processing helix chain 'N' and resid 419 through 424 removed outlier: 4.041A pdb=" N ILE N 424 " --> pdb=" O GLY N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 445 removed outlier: 3.630A pdb=" N ARG N 445 " --> pdb=" O GLU N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 459 removed outlier: 3.801A pdb=" N LEU N 458 " --> pdb=" O GLU N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 483 removed outlier: 3.683A pdb=" N LYS N 471 " --> pdb=" O ASN N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 511 Processing helix chain 'N' and resid 525 through 538 Processing helix chain 'N' and resid 545 through 555 Processing helix chain 'N' and resid 560 through 583 Processing helix chain 'N' and resid 587 through 593 Processing helix chain 'N' and resid 598 through 607 removed outlier: 3.974A pdb=" N ASN N 607 " --> pdb=" O LEU N 603 " (cutoff:3.500A) Processing helix chain 'N' and resid 625 through 629 removed outlier: 3.516A pdb=" N ILE N 629 " --> pdb=" O TRP N 626 " (cutoff:3.500A) Processing helix chain 'N' and resid 632 through 649 Proline residue: N 646 - end of helix Processing helix chain 'N' and resid 649 through 657 removed outlier: 3.752A pdb=" N ARG N 655 " --> pdb=" O GLU N 651 " (cutoff:3.500A) Processing helix chain 'N' and resid 673 through 686 Processing helix chain 'N' and resid 695 through 698 Processing helix chain 'N' and resid 703 through 719 Processing helix chain 'N' and resid 741 through 759 removed outlier: 4.181A pdb=" N VAL N 745 " --> pdb=" O GLY N 741 " (cutoff:3.500A) Processing helix chain 'N' and resid 774 through 778 removed outlier: 3.549A pdb=" N ILE N 778 " --> pdb=" O PRO N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 811 Processing helix chain 'N' and resid 820 through 827 removed outlier: 3.625A pdb=" N LEU N 824 " --> pdb=" O ASP N 820 " (cutoff:3.500A) Processing helix chain 'N' and resid 832 through 851 Processing helix chain 'N' and resid 858 through 869 Processing helix chain 'N' and resid 874 through 888 removed outlier: 3.950A pdb=" N ARG N 878 " --> pdb=" O PRO N 874 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 221 Proline residue: O 219 - end of helix Processing helix chain 'O' and resid 246 through 259 Processing helix chain 'O' and resid 268 through 271 removed outlier: 4.207A pdb=" N GLN O 271 " --> pdb=" O PRO O 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 268 through 271' Processing helix chain 'O' and resid 276 through 294 Processing helix chain 'O' and resid 316 through 333 removed outlier: 3.592A pdb=" N ARG O 320 " --> pdb=" O ALA O 316 " (cutoff:3.500A) Processing helix chain 'O' and resid 346 through 350 Processing helix chain 'O' and resid 351 through 355 Processing helix chain 'O' and resid 370 through 383 Processing helix chain 'O' and resid 392 through 400 removed outlier: 3.605A pdb=" N LEU O 396 " --> pdb=" O ASP O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 404 through 423 Processing helix chain 'O' and resid 433 through 443 removed outlier: 3.550A pdb=" N PHE O 437 " --> pdb=" O ASP O 433 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 466 Processing helix chain 'O' and resid 469 through 480 Processing helix chain 'O' and resid 480 through 486 removed outlier: 3.987A pdb=" N LEU O 484 " --> pdb=" O ILE O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 486 through 494 Processing helix chain 'O' and resid 510 through 521 removed outlier: 3.858A pdb=" N LEU O 514 " --> pdb=" O ALA O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 535 Processing helix chain 'O' and resid 540 through 556 removed outlier: 4.001A pdb=" N LYS O 544 " --> pdb=" O GLY O 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 565 through 570 Processing helix chain 'O' and resid 580 through 595 removed outlier: 3.510A pdb=" N GLU O 584 " --> pdb=" O CYS O 580 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP O 595 " --> pdb=" O LEU O 591 " (cutoff:3.500A) Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 635 through 640 removed outlier: 3.748A pdb=" N LEU O 639 " --> pdb=" O ASP O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 654 through 667 Processing helix chain 'O' and resid 676 through 684 removed outlier: 4.368A pdb=" N LEU O 680 " --> pdb=" O SER O 676 " (cutoff:3.500A) Processing helix chain 'O' and resid 688 through 708 removed outlier: 3.503A pdb=" N ASN O 707 " --> pdb=" O ALA O 703 " (cutoff:3.500A) Processing helix chain 'O' and resid 717 through 726 Processing helix chain 'O' and resid 733 through 745 Processing helix chain 'P' and resid 205 through 221 Proline residue: P 219 - end of helix Processing helix chain 'P' and resid 246 through 259 Processing helix chain 'P' and resid 266 through 271 removed outlier: 3.990A pdb=" N GLN P 271 " --> pdb=" O PRO P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 276 through 296 Processing helix chain 'P' and resid 316 through 333 removed outlier: 3.793A pdb=" N ARG P 320 " --> pdb=" O ALA P 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 350 Processing helix chain 'P' and resid 351 through 355 Processing helix chain 'P' and resid 370 through 383 Processing helix chain 'P' and resid 392 through 400 removed outlier: 3.511A pdb=" N LEU P 396 " --> pdb=" O ASP P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 422 Processing helix chain 'P' and resid 433 through 444 Processing helix chain 'P' and resid 469 through 480 Processing helix chain 'P' and resid 481 through 490 removed outlier: 4.110A pdb=" N LYS P 485 " --> pdb=" O GLU P 481 " (cutoff:3.500A) Proline residue: P 487 - end of helix removed outlier: 3.515A pdb=" N PHE P 490 " --> pdb=" O PHE P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 521 removed outlier: 3.921A pdb=" N LEU P 514 " --> pdb=" O ALA P 510 " (cutoff:3.500A) Processing helix chain 'P' and resid 530 through 535 Processing helix chain 'P' and resid 541 through 556 Processing helix chain 'P' and resid 565 through 570 Processing helix chain 'P' and resid 581 through 594 Processing helix chain 'P' and resid 630 through 634 Processing helix chain 'P' and resid 635 through 640 Processing helix chain 'P' and resid 654 through 666 Processing helix chain 'P' and resid 676 through 684 removed outlier: 3.867A pdb=" N LEU P 680 " --> pdb=" O SER P 676 " (cutoff:3.500A) Processing helix chain 'P' and resid 688 through 707 Processing helix chain 'P' and resid 715 through 726 removed outlier: 4.202A pdb=" N PHE P 719 " --> pdb=" O LYS P 715 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS P 724 " --> pdb=" O LEU P 720 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR P 725 " --> pdb=" O LYS P 721 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 745 Processing helix chain 'A' and resid 5 through 51 Proline residue: A 19 - end of helix removed outlier: 3.819A pdb=" N CYS A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 69 through 117 removed outlier: 4.346A pdb=" N LYS A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 134 through 161 Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.764A pdb=" N ASP A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'B' and resid 7 through 52 Proline residue: B 19 - end of helix Proline residue: B 37 - end of helix Processing helix chain 'B' and resid 60 through 65 removed outlier: 4.036A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 117 Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.103A pdb=" N GLN B 127 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.782A pdb=" N TYR B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.699A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 3.641A pdb=" N SER B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.390A pdb=" N PHE B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 58 Processing helix chain 'C' and resid 88 through 124 Processing helix chain 'C' and resid 142 through 171 Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.818A pdb=" N THR C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 removed outlier: 3.760A pdb=" N LEU C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 57 Processing helix chain 'D' and resid 86 through 123 Processing helix chain 'D' and resid 142 through 171 removed outlier: 4.095A pdb=" N TYR D 146 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.853A pdb=" N THR D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 4.030A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 156 through 169 removed outlier: 3.708A pdb=" N THR E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 186 removed outlier: 3.925A pdb=" N GLY E 185 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG E 186 " --> pdb=" O PHE E 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 182 through 186' Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.761A pdb=" N SER F 66 " --> pdb=" O THR F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 182 through 186 removed outlier: 3.759A pdb=" N GLY G 185 " --> pdb=" O THR G 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 186 " --> pdb=" O PHE G 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 182 through 186' Processing helix chain 'H' and resid 60 through 66 removed outlier: 3.930A pdb=" N SER H 66 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'I' and resid 20 through 26 removed outlier: 4.000A pdb=" N THR I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 127 through 139 removed outlier: 3.889A pdb=" N VAL I 131 " --> pdb=" O ASN I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 removed outlier: 4.393A pdb=" N GLY J 25 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 124 through 128 removed outlier: 4.371A pdb=" N ASN J 127 " --> pdb=" O GLY J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 139 Processing sheet with id=AA1, first strand: chain 'K' and resid 498 through 499 removed outlier: 8.169A pdb=" N THR K 499 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU K 392 " --> pdb=" O THR K 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 414 through 419 removed outlier: 6.465A pdb=" N TYR K 414 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE K 451 " --> pdb=" O TYR K 414 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER K 416 " --> pdb=" O PHE K 451 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP K 453 " --> pdb=" O SER K 416 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE K 418 " --> pdb=" O ASP K 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 689 through 690 removed outlier: 3.528A pdb=" N LEU K 690 " --> pdb=" O ILE K 723 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR K 767 " --> pdb=" O SER K 722 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE K 724 " --> pdb=" O THR K 767 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU K 769 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL K 664 " --> pdb=" O ILE K 768 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 770 " --> pdb=" O VAL K 664 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY K 663 " --> pdb=" O ARG K 790 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE K 792 " --> pdb=" O GLY K 663 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU K 665 " --> pdb=" O ILE K 792 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 414 through 418 removed outlier: 6.154A pdb=" N TYR L 414 " --> pdb=" O ILE L 449 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE L 451 " --> pdb=" O TYR L 414 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER L 416 " --> pdb=" O PHE L 451 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP L 453 " --> pdb=" O SER L 416 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE L 418 " --> pdb=" O ASP L 453 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU L 494 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY L 497 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 499 " --> pdb=" O LEU L 392 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY L 389 " --> pdb=" O LYS L 517 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE L 519 " --> pdb=" O GLY L 389 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 391 " --> pdb=" O ILE L 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 689 through 690 removed outlier: 6.422A pdb=" N LEU L 690 " --> pdb=" O PHE L 725 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASP L 727 " --> pdb=" O LEU L 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE L 724 " --> pdb=" O LEU L 769 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA L 771 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE L 726 " --> pdb=" O ALA L 771 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL L 664 " --> pdb=" O ILE L 768 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY L 663 " --> pdb=" O ARG L 790 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE L 792 " --> pdb=" O GLY L 663 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU L 665 " --> pdb=" O ILE L 792 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 390 through 393 Processing sheet with id=AA7, first strand: chain 'M' and resid 414 through 418 removed outlier: 3.611A pdb=" N SER M 416 " --> pdb=" O ILE M 449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE M 451 " --> pdb=" O SER M 416 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 418 " --> pdb=" O PHE M 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 688 through 689 removed outlier: 6.374A pdb=" N ASN M 688 " --> pdb=" O ILE M 723 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER M 722 " --> pdb=" O THR M 767 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LEU M 769 " --> pdb=" O SER M 722 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL M 664 " --> pdb=" O ILE M 768 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY M 663 " --> pdb=" O ILE M 788 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 692 through 693 removed outlier: 6.911A pdb=" N ILE M 692 " --> pdb=" O ASP M 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 414 through 418 removed outlier: 3.564A pdb=" N PHE N 451 " --> pdb=" O SER N 416 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP N 453 " --> pdb=" O ILE N 418 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 494 " --> pdb=" O SER N 448 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL N 390 " --> pdb=" O VAL N 495 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY N 497 " --> pdb=" O VAL N 390 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE N 519 " --> pdb=" O GLY N 389 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU N 391 " --> pdb=" O ILE N 519 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 689 through 693 removed outlier: 6.259A pdb=" N LEU N 690 " --> pdb=" O PHE N 725 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP N 727 " --> pdb=" O LEU N 690 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE N 692 " --> pdb=" O ASP N 727 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE N 724 " --> pdb=" O LEU N 769 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA N 771 " --> pdb=" O ILE N 724 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE N 726 " --> pdb=" O ALA N 771 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL N 664 " --> pdb=" O ALA N 770 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR N 772 " --> pdb=" O VAL N 664 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU N 666 " --> pdb=" O THR N 772 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 341 through 344 removed outlier: 6.373A pdb=" N VAL O 237 " --> pdb=" O GLY O 342 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR O 344 " --> pdb=" O VAL O 237 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU O 239 " --> pdb=" O THR O 344 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU O 238 " --> pdb=" O VAL O 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'O' and resid 265 through 266 removed outlier: 7.261A pdb=" N VAL O 265 " --> pdb=" O ASP O 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 525 through 529 removed outlier: 6.313A pdb=" N VAL O 501 " --> pdb=" O ALA O 626 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR O 628 " --> pdb=" O VAL O 501 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU O 503 " --> pdb=" O THR O 628 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE O 648 " --> pdb=" O GLY O 500 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU O 502 " --> pdb=" O ILE O 648 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 263 through 265 removed outlier: 4.118A pdb=" N LEU P 263 " --> pdb=" O LEU P 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE P 301 " --> pdb=" O LEU P 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL P 265 " --> pdb=" O PHE P 301 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP P 303 " --> pdb=" O VAL P 265 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER P 298 " --> pdb=" O VAL P 339 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 341 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU P 300 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA P 343 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU P 302 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU P 238 " --> pdb=" O VAL P 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 525 through 529 removed outlier: 6.622A pdb=" N SER P 525 " --> pdb=" O ILE P 560 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE P 562 " --> pdb=" O SER P 525 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL P 527 " --> pdb=" O PHE P 562 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA P 559 " --> pdb=" O MET P 623 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE P 625 " --> pdb=" O ALA P 559 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU P 561 " --> pdb=" O ILE P 625 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA P 627 " --> pdb=" O LEU P 561 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU P 563 " --> pdb=" O ALA P 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL P 501 " --> pdb=" O ILE P 624 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR P 628 " --> pdb=" O LEU P 503 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY P 500 " --> pdb=" O LYS P 646 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE P 648 " --> pdb=" O GLY P 500 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU P 502 " --> pdb=" O ILE P 648 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 69 removed outlier: 5.901A pdb=" N ILE E 68 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL E 111 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR E 47 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU E 113 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR E 49 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 201 through 203 removed outlier: 5.820A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 325 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 201 through 203 removed outlier: 5.820A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 46 through 50 removed outlier: 3.528A pdb=" N LEU F 113 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AC4, first strand: chain 'F' and resid 178 through 183 removed outlier: 3.609A pdb=" N ARG F 186 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP F 145 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL F 195 " --> pdb=" O GLU F 143 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU F 143 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 47 removed outlier: 5.945A pdb=" N ILE G 68 " --> pdb=" O TRP G 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 178 through 179 removed outlier: 3.701A pdb=" N LEU G 190 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 178 through 179 removed outlier: 3.701A pdb=" N LEU G 190 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 192 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA G 147 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG G 194 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU G 142 " --> pdb=" O ARG G 331 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN G 333 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET G 144 " --> pdb=" O ASN G 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.802A pdb=" N THR H 47 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU H 113 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR H 49 " --> pdb=" O LEU H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AD1, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.475A pdb=" N ALA H 137 " --> pdb=" O PHE H 323 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE H 325 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU H 139 " --> pdb=" O PHE H 325 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR H 324 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 195 through 196 removed outlier: 6.341A pdb=" N MET H 144 " --> pdb=" O ASN H 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 182 through 183 removed outlier: 3.630A pdb=" N ARG H 186 " --> pdb=" O PHE H 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'I' and resid 164 through 168 removed outlier: 5.851A pdb=" N ILE I 165 " --> pdb=" O TRP I 113 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP I 113 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL I 110 " --> pdb=" O SER I 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AD7, first strand: chain 'J' and resid 15 through 16 removed outlier: 5.904A pdb=" N LYS J 15 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU J 74 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN J 73 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 15 through 16 removed outlier: 5.904A pdb=" N LYS J 15 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU J 74 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN J 73 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS J 78 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS J 148 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU J 163 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL J 115 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE J 165 " --> pdb=" O TRP J 113 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP J 113 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL J 110 " --> pdb=" O ARG J 183 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5439 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: 5.67 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6568 1.31 - 1.44: 8958 1.44 - 1.57: 23219 1.57 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 39017 Sorted by residual: bond pdb=" N PRO P 483 " pdb=" CD PRO P 483 " ideal model delta sigma weight residual 1.473 1.329 0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" CA LEU A 168 " pdb=" C LEU A 168 " ideal model delta sigma weight residual 1.522 1.458 0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" N LYS G 58 " pdb=" CA LYS G 58 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.28e+00 ... (remaining 39012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 52669 4.34 - 8.67: 168 8.67 - 13.01: 4 13.01 - 17.35: 1 17.35 - 21.68: 1 Bond angle restraints: 52843 Sorted by residual: angle pdb=" C HIS A 186 " pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " ideal model delta sigma weight residual 109.54 125.39 -15.85 1.84e+00 2.95e-01 7.42e+01 angle pdb=" C ILE G 59 " pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 125.00 103.32 21.68 4.10e+00 5.95e-02 2.80e+01 angle pdb=" CA ASP G 56 " pdb=" C ASP G 56 " pdb=" N ASP G 57 " ideal model delta sigma weight residual 117.23 110.91 6.32 1.31e+00 5.83e-01 2.32e+01 angle pdb=" C ILE G 59 " pdb=" CA ILE G 59 " pdb=" CB ILE G 59 " ideal model delta sigma weight residual 111.36 119.46 -8.10 1.82e+00 3.02e-01 1.98e+01 angle pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " pdb=" CG HIS A 186 " ideal model delta sigma weight residual 113.80 118.00 -4.20 1.00e+00 1.00e+00 1.77e+01 ... (remaining 52838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 21861 18.47 - 36.93: 1931 36.93 - 55.40: 242 55.40 - 73.87: 43 73.87 - 92.33: 33 Dihedral angle restraints: 24110 sinusoidal: 9820 harmonic: 14290 Sorted by residual: dihedral pdb=" C ILE G 59 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " pdb=" CB ILE G 59 " ideal model delta harmonic sigma weight residual -122.00 -138.79 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C HIS A 186 " pdb=" N HIS A 186 " pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " ideal model delta harmonic sigma weight residual -122.60 -138.07 15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" CA GLU G 53 " pdb=" C GLU G 53 " pdb=" N LYS G 54 " pdb=" CA LYS G 54 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 24107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5763 0.089 - 0.178: 396 0.178 - 0.267: 8 0.267 - 0.357: 0 0.357 - 0.446: 2 Chirality restraints: 6169 Sorted by residual: chirality pdb=" CA ILE G 59 " pdb=" N ILE G 59 " pdb=" C ILE G 59 " pdb=" CB ILE G 59 " both_signs ideal model delta sigma weight residual False 2.43 1.99 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA HIS A 186 " pdb=" N HIS A 186 " pdb=" C HIS A 186 " pdb=" CB HIS A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA THR I 169 " pdb=" N THR I 169 " pdb=" C THR I 169 " pdb=" CB THR I 169 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 6166 not shown) Planarity restraints: 6842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 59 " 0.084 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PRO G 60 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 56 " 0.023 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP G 56 " -0.083 2.00e-02 2.50e+03 pdb=" O ASP G 56 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP G 57 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 185 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU A 185 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A 185 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 186 " 0.026 2.00e-02 2.50e+03 ... (remaining 6839 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 21 2.01 - 2.73: 4291 2.73 - 3.46: 61288 3.46 - 4.18: 87686 4.18 - 4.90: 147311 Nonbonded interactions: 300597 Sorted by model distance: nonbonded pdb=" O LEU P 701 " pdb=" OE1 GLN P 705 " model vdw 1.290 3.040 nonbonded pdb=" CD1 LEU B 195 " pdb=" CD1 ILE G 59 " model vdw 1.310 3.880 nonbonded pdb=" O GLN M 752 " pdb=" OE1 GLU M 756 " model vdw 1.568 3.040 nonbonded pdb=" CB LEU B 195 " pdb=" CG2 ILE G 59 " model vdw 1.578 3.860 nonbonded pdb=" O GLN P 287 " pdb=" OE1 GLU P 291 " model vdw 1.580 3.040 ... (remaining 300592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 201) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 19 through 58 or resid 86 through 208)) selection = (chain 'D' and (resid 19 through 58 or resid 86 through 125 or resid 138 or resi \ d 141 through 208)) } ncs_group { reference = (chain 'E' and (resid 45 through 202 or resid 318 through 334)) selection = chain 'F' selection = (chain 'G' and (resid 45 through 202 or resid 318 through 334)) selection = (chain 'H' and (resid 45 through 202 or resid 318 through 334)) } ncs_group { reference = (chain 'I' and resid 12 through 192) selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 350 through 874) selection = (chain 'L' and resid 350 through 874) selection = (chain 'M' and resid 350 through 874) selection = (chain 'N' and resid 350 through 874) } ncs_group { reference = (chain 'O' and (resid 201 through 603 or resid 617 through 746)) selection = (chain 'P' and (resid 201 through 449 or resid 457 through 746)) } 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=0.00 max=1.00 mean=0.62 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: 3.510 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 30.250 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.007 0.319 39020 Z= 0.362 Angle : 0.799 21.684 52843 Z= 0.435 Chirality : 0.046 0.446 6169 Planarity : 0.005 0.141 6842 Dihedral : 13.997 92.333 14860 Min Nonbonded Distance : 1.290 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.89 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.53 (0.10), residues: 4920 helix: -2.29 (0.09), residues: 2322 sheet: -2.80 (0.19), residues: 505 loop : -3.88 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 501 TYR 0.027 0.002 TYR M 667 PHE 0.022 0.002 PHE G 325 TRP 0.047 0.002 TRP B 28 HIS 0.009 0.001 HIS M 557 Details of bonding type rmsd covalent geometry : bond 0.00627 (39017) covalent geometry : angle 0.79911 (52843) hydrogen bonds : bond 0.14612 ( 1878) hydrogen bonds : angle 6.77387 ( 5439) Misc. bond : bond 0.23331 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8348 (ttm170) REVERT: A 138 MET cc_start: 0.9054 (mmm) cc_final: 0.8661 (tpp) REVERT: B 172 GLN cc_start: 0.8888 (tt0) cc_final: 0.8408 (tp40) REVERT: B 189 LEU cc_start: 0.8397 (mt) cc_final: 0.8166 (mt) REVERT: B 192 ASP cc_start: 0.8755 (m-30) cc_final: 0.8486 (m-30) REVERT: C 155 MET cc_start: 0.9259 (mtm) cc_final: 0.8960 (mtp) REVERT: D 29 ASP cc_start: 0.9186 (m-30) cc_final: 0.8976 (m-30) REVERT: G 58 LYS cc_start: 0.8615 (tttt) cc_final: 0.7948 (ptpt) REVERT: G 67 LEU cc_start: 0.8579 (mt) cc_final: 0.8300 (tp) REVERT: G 118 GLN cc_start: 0.7806 (mt0) cc_final: 0.7500 (mt0) REVERT: I 133 GLU cc_start: 0.8558 (tt0) cc_final: 0.8187 (tt0) REVERT: J 132 LEU cc_start: 0.8727 (tp) cc_final: 0.8403 (tt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.2403 time to fit residues: 194.5334 Evaluate side-chains 355 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 0.0670 chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 0.0470 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 77 GLN A 148 HIS A 186 HIS ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN B 148 HIS C 26 ASN C 31 HIS D 31 HIS D 138 HIS D 144 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098332 restraints weight = 135115.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097242 restraints weight = 100857.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098079 restraints weight = 98679.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098099 restraints weight = 79261.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098482 restraints weight = 71102.185| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39020 Z= 0.155 Angle : 0.701 8.771 52843 Z= 0.354 Chirality : 0.045 0.232 6169 Planarity : 0.005 0.105 6842 Dihedral : 5.328 26.900 5355 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.38 % Rotamer: Outliers : 0.17 % Allowed : 6.00 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.11), residues: 4920 helix: -0.56 (0.10), residues: 2387 sheet: -2.28 (0.19), residues: 540 loop : -3.10 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 643 TYR 0.025 0.002 TYR O 649 PHE 0.026 0.002 PHE P 486 TRP 0.035 0.002 TRP G 101 HIS 0.007 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00331 (39017) covalent geometry : angle 0.70134 (52843) hydrogen bonds : bond 0.05293 ( 1878) hydrogen bonds : angle 5.34867 ( 5439) Misc. bond : bond 0.00175 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 488 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8263 (ttm170) REVERT: A 138 MET cc_start: 0.9004 (mmm) cc_final: 0.8255 (mmm) REVERT: A 184 ASP cc_start: 0.8646 (t0) cc_final: 0.8093 (t0) REVERT: B 192 ASP cc_start: 0.8474 (m-30) cc_final: 0.8131 (m-30) REVERT: B 194 LEU cc_start: 0.9170 (mt) cc_final: 0.8968 (tp) REVERT: C 25 ASP cc_start: 0.9261 (m-30) cc_final: 0.9004 (m-30) REVERT: C 29 ASP cc_start: 0.9084 (m-30) cc_final: 0.8816 (m-30) REVERT: C 100 ASP cc_start: 0.8823 (m-30) cc_final: 0.8514 (m-30) REVERT: C 155 MET cc_start: 0.9028 (mtm) cc_final: 0.8714 (mtp) REVERT: C 184 SER cc_start: 0.9668 (p) cc_final: 0.9301 (t) REVERT: D 25 ASP cc_start: 0.9354 (m-30) cc_final: 0.9117 (m-30) REVERT: D 29 ASP cc_start: 0.9107 (m-30) cc_final: 0.8791 (m-30) REVERT: G 118 GLN cc_start: 0.7780 (mt0) cc_final: 0.7456 (mt0) REVERT: J 132 LEU cc_start: 0.8677 (tp) cc_final: 0.8358 (tt) outliers start: 7 outliers final: 3 residues processed: 495 average time/residue: 0.2133 time to fit residues: 171.0565 Evaluate side-chains 370 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 367 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 185 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 466 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 462 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.116022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097297 restraints weight = 134669.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095756 restraints weight = 95859.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096532 restraints weight = 89759.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096771 restraints weight = 72151.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096839 restraints weight = 65935.744| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39020 Z= 0.204 Angle : 0.709 10.987 52843 Z= 0.358 Chirality : 0.045 0.281 6169 Planarity : 0.006 0.091 6842 Dihedral : 5.263 34.538 5355 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.19 % Favored : 90.77 % Rotamer: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.12), residues: 4920 helix: -0.07 (0.10), residues: 2397 sheet: -1.93 (0.19), residues: 549 loop : -2.88 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 445 TYR 0.027 0.002 TYR M 667 PHE 0.022 0.002 PHE P 486 TRP 0.026 0.002 TRP B 28 HIS 0.018 0.001 HIS K 861 Details of bonding type rmsd covalent geometry : bond 0.00449 (39017) covalent geometry : angle 0.70884 (52843) hydrogen bonds : bond 0.05081 ( 1878) hydrogen bonds : angle 5.22470 ( 5439) Misc. bond : bond 0.00076 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8298 (ttm170) REVERT: A 184 ASP cc_start: 0.8660 (t0) cc_final: 0.8100 (t0) REVERT: B 172 GLN cc_start: 0.8882 (tt0) cc_final: 0.8254 (tp40) REVERT: B 189 LEU cc_start: 0.8313 (mt) cc_final: 0.8107 (mt) REVERT: C 25 ASP cc_start: 0.9271 (m-30) cc_final: 0.9032 (m-30) REVERT: C 29 ASP cc_start: 0.9161 (m-30) cc_final: 0.8904 (m-30) REVERT: C 100 ASP cc_start: 0.8871 (m-30) cc_final: 0.8572 (m-30) REVERT: C 155 MET cc_start: 0.9066 (mtm) cc_final: 0.8764 (mtp) REVERT: D 25 ASP cc_start: 0.9367 (m-30) cc_final: 0.9140 (m-30) REVERT: D 29 ASP cc_start: 0.9192 (m-30) cc_final: 0.8866 (m-30) REVERT: G 118 GLN cc_start: 0.7836 (mt0) cc_final: 0.7401 (mt0) REVERT: J 132 LEU cc_start: 0.8759 (tp) cc_final: 0.8408 (tt) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.2163 time to fit residues: 156.5867 Evaluate side-chains 339 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 460 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 chunk 325 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096240 restraints weight = 130216.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.095410 restraints weight = 86133.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096238 restraints weight = 77254.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096378 restraints weight = 65940.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096658 restraints weight = 57995.059| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39020 Z= 0.203 Angle : 0.699 11.290 52843 Z= 0.352 Chirality : 0.045 0.242 6169 Planarity : 0.005 0.092 6842 Dihedral : 5.224 35.764 5355 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.96 % Favored : 91.00 % Rotamer: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 4920 helix: 0.16 (0.10), residues: 2400 sheet: -1.73 (0.20), residues: 548 loop : -2.71 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 643 TYR 0.026 0.002 TYR M 667 PHE 0.034 0.002 PHE P 486 TRP 0.024 0.002 TRP B 28 HIS 0.012 0.001 HIS K 861 Details of bonding type rmsd covalent geometry : bond 0.00448 (39017) covalent geometry : angle 0.69934 (52843) hydrogen bonds : bond 0.04892 ( 1878) hydrogen bonds : angle 5.13727 ( 5439) Misc. bond : bond 0.00041 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8281 (ttm170) REVERT: A 184 ASP cc_start: 0.8751 (t0) cc_final: 0.8178 (t0) REVERT: B 172 GLN cc_start: 0.8958 (tt0) cc_final: 0.8254 (tp40) REVERT: B 189 LEU cc_start: 0.8219 (mt) cc_final: 0.7981 (mt) REVERT: C 25 ASP cc_start: 0.9286 (m-30) cc_final: 0.9044 (m-30) REVERT: C 29 ASP cc_start: 0.9189 (m-30) cc_final: 0.8926 (m-30) REVERT: C 100 ASP cc_start: 0.8932 (m-30) cc_final: 0.8619 (m-30) REVERT: C 155 MET cc_start: 0.9040 (mtm) cc_final: 0.8717 (mtp) REVERT: D 25 ASP cc_start: 0.9361 (m-30) cc_final: 0.9129 (m-30) REVERT: D 29 ASP cc_start: 0.9191 (m-30) cc_final: 0.8874 (m-30) REVERT: D 100 ASP cc_start: 0.8927 (m-30) cc_final: 0.8594 (m-30) REVERT: J 132 LEU cc_start: 0.8761 (tp) cc_final: 0.8436 (tt) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.2160 time to fit residues: 151.7703 Evaluate side-chains 341 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 96 optimal weight: 9.9990 chunk 237 optimal weight: 0.8980 chunk 255 optimal weight: 0.0030 chunk 202 optimal weight: 4.9990 chunk 320 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 462 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 309 optimal weight: 40.0000 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097122 restraints weight = 128810.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097042 restraints weight = 83708.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098030 restraints weight = 67187.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098177 restraints weight = 58227.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098752 restraints weight = 50198.173| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39020 Z= 0.128 Angle : 0.647 9.680 52843 Z= 0.322 Chirality : 0.044 0.227 6169 Planarity : 0.005 0.091 6842 Dihedral : 4.941 33.775 5355 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.12), residues: 4920 helix: 0.52 (0.11), residues: 2408 sheet: -1.59 (0.20), residues: 566 loop : -2.43 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG M 445 TYR 0.021 0.002 TYR M 667 PHE 0.017 0.001 PHE A 18 TRP 0.031 0.002 TRP B 28 HIS 0.012 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00275 (39017) covalent geometry : angle 0.64726 (52843) hydrogen bonds : bond 0.04458 ( 1878) hydrogen bonds : angle 4.76098 ( 5439) Misc. bond : bond 0.00990 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8123 (ttm170) REVERT: A 64 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8871 (ttp-110) REVERT: A 101 MET cc_start: 0.8023 (ttm) cc_final: 0.7812 (ttm) REVERT: A 184 ASP cc_start: 0.8496 (t0) cc_final: 0.8023 (t0) REVERT: B 64 ARG cc_start: 0.9500 (ttm170) cc_final: 0.8939 (ttp-110) REVERT: B 172 GLN cc_start: 0.8948 (tt0) cc_final: 0.8180 (tp40) REVERT: C 25 ASP cc_start: 0.9249 (m-30) cc_final: 0.8547 (t0) REVERT: C 29 ASP cc_start: 0.9128 (m-30) cc_final: 0.8700 (m-30) REVERT: C 34 ILE cc_start: 0.9473 (mm) cc_final: 0.9197 (mm) REVERT: C 100 ASP cc_start: 0.8892 (m-30) cc_final: 0.8562 (m-30) REVERT: C 155 MET cc_start: 0.8933 (mtm) cc_final: 0.8622 (mtp) REVERT: D 25 ASP cc_start: 0.9342 (m-30) cc_final: 0.9089 (m-30) REVERT: D 29 ASP cc_start: 0.9128 (m-30) cc_final: 0.8785 (m-30) REVERT: D 100 ASP cc_start: 0.8850 (m-30) cc_final: 0.8537 (m-30) REVERT: D 184 SER cc_start: 0.9622 (p) cc_final: 0.9338 (t) REVERT: H 169 ASP cc_start: 0.8714 (t70) cc_final: 0.8420 (t0) REVERT: J 132 LEU cc_start: 0.8730 (tp) cc_final: 0.8424 (tt) outliers start: 2 outliers final: 1 residues processed: 482 average time/residue: 0.2294 time to fit residues: 180.2709 Evaluate side-chains 350 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 103 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 353 optimal weight: 0.4980 chunk 157 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 451 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098649 restraints weight = 135287.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098325 restraints weight = 93507.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098796 restraints weight = 86909.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099161 restraints weight = 69298.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099206 restraints weight = 63516.957| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39020 Z= 0.135 Angle : 0.651 9.976 52843 Z= 0.323 Chirality : 0.044 0.408 6169 Planarity : 0.005 0.091 6842 Dihedral : 4.832 32.524 5355 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.87 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.12), residues: 4920 helix: 0.68 (0.11), residues: 2399 sheet: -1.47 (0.20), residues: 589 loop : -2.27 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 445 TYR 0.034 0.002 TYR M 667 PHE 0.027 0.001 PHE P 441 TRP 0.031 0.002 TRP B 28 HIS 0.009 0.001 HIS H 69 Details of bonding type rmsd covalent geometry : bond 0.00296 (39017) covalent geometry : angle 0.65097 (52843) hydrogen bonds : bond 0.04318 ( 1878) hydrogen bonds : angle 4.67531 ( 5439) Misc. bond : bond 0.00102 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8107 (mtm-85) REVERT: A 64 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8839 (ttp-110) REVERT: A 101 MET cc_start: 0.7949 (ttm) cc_final: 0.7741 (ttm) REVERT: A 138 MET cc_start: 0.9097 (mmm) cc_final: 0.8825 (tpp) REVERT: A 184 ASP cc_start: 0.8473 (t0) cc_final: 0.7991 (t0) REVERT: C 25 ASP cc_start: 0.9211 (m-30) cc_final: 0.8510 (t0) REVERT: C 29 ASP cc_start: 0.9075 (m-30) cc_final: 0.8671 (m-30) REVERT: C 34 ILE cc_start: 0.9470 (mm) cc_final: 0.9178 (mm) REVERT: C 100 ASP cc_start: 0.8795 (m-30) cc_final: 0.8475 (m-30) REVERT: D 25 ASP cc_start: 0.9315 (m-30) cc_final: 0.9085 (m-30) REVERT: D 29 ASP cc_start: 0.9115 (m-30) cc_final: 0.8803 (m-30) REVERT: D 100 ASP cc_start: 0.8778 (m-30) cc_final: 0.8484 (m-30) REVERT: H 169 ASP cc_start: 0.8665 (t70) cc_final: 0.8424 (t0) REVERT: J 132 LEU cc_start: 0.8761 (tp) cc_final: 0.8448 (tt) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2277 time to fit residues: 171.5797 Evaluate side-chains 356 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 396 optimal weight: 4.9990 chunk 482 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 356 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 423 optimal weight: 0.0970 chunk 276 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.117348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098090 restraints weight = 132905.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097865 restraints weight = 89775.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.098504 restraints weight = 80936.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098672 restraints weight = 68858.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099012 restraints weight = 62220.911| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39020 Z= 0.145 Angle : 0.647 8.320 52843 Z= 0.324 Chirality : 0.043 0.239 6169 Planarity : 0.005 0.092 6842 Dihedral : 4.777 33.266 5355 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.72 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.12), residues: 4920 helix: 0.79 (0.11), residues: 2386 sheet: -1.23 (0.20), residues: 558 loop : -2.14 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 445 TYR 0.045 0.002 TYR M 667 PHE 0.026 0.001 PHE P 486 TRP 0.032 0.002 TRP B 28 HIS 0.007 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00322 (39017) covalent geometry : angle 0.64725 (52843) hydrogen bonds : bond 0.04249 ( 1878) hydrogen bonds : angle 4.66543 ( 5439) Misc. bond : bond 0.00097 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8105 (mtm-85) REVERT: A 101 MET cc_start: 0.7956 (ttm) cc_final: 0.7737 (ttm) REVERT: A 138 MET cc_start: 0.9094 (mmm) cc_final: 0.8781 (tpp) REVERT: A 184 ASP cc_start: 0.8419 (t0) cc_final: 0.7931 (t0) REVERT: B 172 GLN cc_start: 0.8861 (tt0) cc_final: 0.8167 (tp40) REVERT: B 184 ASP cc_start: 0.8485 (t70) cc_final: 0.8172 (t0) REVERT: C 25 ASP cc_start: 0.9179 (m-30) cc_final: 0.8479 (t0) REVERT: C 29 ASP cc_start: 0.9023 (m-30) cc_final: 0.8661 (m-30) REVERT: C 34 ILE cc_start: 0.9498 (mm) cc_final: 0.9144 (mm) REVERT: C 100 ASP cc_start: 0.8766 (m-30) cc_final: 0.8450 (m-30) REVERT: C 175 ASP cc_start: 0.8585 (p0) cc_final: 0.8310 (p0) REVERT: D 25 ASP cc_start: 0.9275 (m-30) cc_final: 0.9043 (m-30) REVERT: D 29 ASP cc_start: 0.9032 (m-30) cc_final: 0.8736 (m-30) REVERT: D 100 ASP cc_start: 0.8726 (m-30) cc_final: 0.8436 (m-30) REVERT: D 184 SER cc_start: 0.9565 (t) cc_final: 0.9354 (p) REVERT: J 132 LEU cc_start: 0.8821 (tp) cc_final: 0.8480 (tt) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2279 time to fit residues: 169.1841 Evaluate side-chains 346 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 78 optimal weight: 20.0000 chunk 404 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.116675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.096883 restraints weight = 128615.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096790 restraints weight = 81945.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097603 restraints weight = 66500.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098094 restraints weight = 55116.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098249 restraints weight = 49110.743| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39020 Z= 0.166 Angle : 0.659 10.312 52843 Z= 0.331 Chirality : 0.043 0.247 6169 Planarity : 0.005 0.096 6842 Dihedral : 4.812 33.777 5355 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.89 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.12), residues: 4920 helix: 0.78 (0.11), residues: 2406 sheet: -1.26 (0.20), residues: 566 loop : -2.13 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 445 TYR 0.037 0.002 TYR M 667 PHE 0.029 0.001 PHE P 486 TRP 0.035 0.002 TRP A 28 HIS 0.008 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00368 (39017) covalent geometry : angle 0.65897 (52843) hydrogen bonds : bond 0.04328 ( 1878) hydrogen bonds : angle 4.69437 ( 5439) Misc. bond : bond 0.00052 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8121 (mtm-85) REVERT: A 101 MET cc_start: 0.8118 (ttm) cc_final: 0.7884 (ttm) REVERT: A 138 MET cc_start: 0.9134 (mmm) cc_final: 0.8574 (mmm) REVERT: A 184 ASP cc_start: 0.8617 (t0) cc_final: 0.8071 (t0) REVERT: B 167 ASP cc_start: 0.8208 (p0) cc_final: 0.7885 (p0) REVERT: B 172 GLN cc_start: 0.8937 (tt0) cc_final: 0.8011 (tp40) REVERT: B 184 ASP cc_start: 0.8685 (t70) cc_final: 0.8353 (t0) REVERT: C 25 ASP cc_start: 0.9251 (m-30) cc_final: 0.8559 (t0) REVERT: C 29 ASP cc_start: 0.9112 (m-30) cc_final: 0.8699 (m-30) REVERT: C 34 ILE cc_start: 0.9465 (mm) cc_final: 0.9183 (mm) REVERT: C 100 ASP cc_start: 0.8887 (m-30) cc_final: 0.8566 (m-30) REVERT: D 25 ASP cc_start: 0.9322 (m-30) cc_final: 0.9082 (m-30) REVERT: D 29 ASP cc_start: 0.9096 (m-30) cc_final: 0.8769 (m-30) REVERT: D 100 ASP cc_start: 0.8846 (m-30) cc_final: 0.8517 (m-30) REVERT: D 184 SER cc_start: 0.9580 (t) cc_final: 0.9364 (p) REVERT: J 132 LEU cc_start: 0.8781 (tp) cc_final: 0.8442 (tt) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.2205 time to fit residues: 164.3328 Evaluate side-chains 350 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 378 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 402 optimal weight: 0.1980 chunk 24 optimal weight: 8.9990 chunk 420 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 263 optimal weight: 50.0000 chunk 7 optimal weight: 20.0000 chunk 395 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.117329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098580 restraints weight = 134816.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097898 restraints weight = 94297.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098364 restraints weight = 89994.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098842 restraints weight = 71021.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099052 restraints weight = 63746.889| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39020 Z= 0.142 Angle : 0.645 11.432 52843 Z= 0.322 Chirality : 0.043 0.245 6169 Planarity : 0.005 0.093 6842 Dihedral : 4.731 33.476 5355 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4920 helix: 0.90 (0.11), residues: 2398 sheet: -1.15 (0.20), residues: 561 loop : -2.02 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 445 TYR 0.037 0.002 TYR M 667 PHE 0.025 0.001 PHE P 486 TRP 0.031 0.001 TRP B 28 HIS 0.008 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00317 (39017) covalent geometry : angle 0.64530 (52843) hydrogen bonds : bond 0.04195 ( 1878) hydrogen bonds : angle 4.57550 ( 5439) Misc. bond : bond 0.00036 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8099 (mtm-85) REVERT: A 101 MET cc_start: 0.8043 (ttm) cc_final: 0.7814 (ttm) REVERT: A 138 MET cc_start: 0.9152 (mmm) cc_final: 0.8534 (mmm) REVERT: A 184 ASP cc_start: 0.8462 (t0) cc_final: 0.7956 (t0) REVERT: B 86 ASP cc_start: 0.8464 (m-30) cc_final: 0.8195 (t70) REVERT: B 167 ASP cc_start: 0.8317 (p0) cc_final: 0.7943 (p0) REVERT: B 184 ASP cc_start: 0.8616 (t70) cc_final: 0.8278 (t0) REVERT: C 25 ASP cc_start: 0.9220 (m-30) cc_final: 0.8535 (t0) REVERT: C 29 ASP cc_start: 0.9042 (m-30) cc_final: 0.8685 (m-30) REVERT: C 34 ILE cc_start: 0.9458 (mm) cc_final: 0.9156 (mm) REVERT: C 100 ASP cc_start: 0.8797 (m-30) cc_final: 0.8469 (m-30) REVERT: C 155 MET cc_start: 0.9122 (ttt) cc_final: 0.8863 (ttt) REVERT: D 25 ASP cc_start: 0.9310 (m-30) cc_final: 0.8654 (t0) REVERT: D 29 ASP cc_start: 0.9059 (m-30) cc_final: 0.8636 (m-30) REVERT: D 100 ASP cc_start: 0.8783 (m-30) cc_final: 0.8443 (m-30) REVERT: J 132 LEU cc_start: 0.8813 (tp) cc_final: 0.8483 (tt) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2212 time to fit residues: 162.5857 Evaluate side-chains 350 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 382 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 403 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 462 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098110 restraints weight = 135072.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097204 restraints weight = 93692.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097976 restraints weight = 92101.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098041 restraints weight = 75090.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098386 restraints weight = 67426.571| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39020 Z= 0.193 Angle : 0.682 11.910 52843 Z= 0.342 Chirality : 0.044 0.266 6169 Planarity : 0.005 0.093 6842 Dihedral : 4.808 34.376 5355 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.12), residues: 4920 helix: 0.80 (0.11), residues: 2410 sheet: -1.26 (0.20), residues: 588 loop : -2.04 (0.15), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 860 TYR 0.036 0.002 TYR M 667 PHE 0.023 0.001 PHE P 486 TRP 0.036 0.002 TRP A 28 HIS 0.008 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00431 (39017) covalent geometry : angle 0.68217 (52843) hydrogen bonds : bond 0.04390 ( 1878) hydrogen bonds : angle 4.72602 ( 5439) Misc. bond : bond 0.00037 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8090 (mtm-85) REVERT: A 101 MET cc_start: 0.7905 (ttm) cc_final: 0.7694 (ttm) REVERT: A 138 MET cc_start: 0.9112 (mmm) cc_final: 0.8792 (mmm) REVERT: A 184 ASP cc_start: 0.8476 (t0) cc_final: 0.7953 (t0) REVERT: B 167 ASP cc_start: 0.8104 (p0) cc_final: 0.7701 (p0) REVERT: B 192 ASP cc_start: 0.8365 (m-30) cc_final: 0.8059 (m-30) REVERT: C 25 ASP cc_start: 0.9148 (m-30) cc_final: 0.8452 (t0) REVERT: C 29 ASP cc_start: 0.8983 (m-30) cc_final: 0.8672 (m-30) REVERT: C 34 ILE cc_start: 0.9483 (mm) cc_final: 0.9087 (mm) REVERT: C 100 ASP cc_start: 0.8760 (m-30) cc_final: 0.8445 (m-30) REVERT: C 155 MET cc_start: 0.9143 (ttt) cc_final: 0.8876 (ttt) REVERT: D 25 ASP cc_start: 0.9251 (m-30) cc_final: 0.9023 (m-30) REVERT: D 29 ASP cc_start: 0.8985 (m-30) cc_final: 0.8695 (m-30) REVERT: D 53 ASN cc_start: 0.8933 (m-40) cc_final: 0.8514 (m110) REVERT: D 100 ASP cc_start: 0.8710 (m-30) cc_final: 0.8401 (m-30) REVERT: J 132 LEU cc_start: 0.8827 (tp) cc_final: 0.8446 (tt) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.2527 time to fit residues: 176.9671 Evaluate side-chains 338 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 405 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 395 optimal weight: 0.6980 chunk 263 optimal weight: 40.0000 chunk 332 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 451 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 316 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.117221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097789 restraints weight = 132038.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096612 restraints weight = 87772.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097544 restraints weight = 82478.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097769 restraints weight = 68005.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098234 restraints weight = 59958.607| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39020 Z= 0.141 Angle : 0.654 11.443 52843 Z= 0.325 Chirality : 0.043 0.250 6169 Planarity : 0.005 0.091 6842 Dihedral : 4.721 33.629 5355 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.12), residues: 4920 helix: 0.92 (0.11), residues: 2410 sheet: -1.11 (0.20), residues: 577 loop : -1.97 (0.15), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 119 TYR 0.035 0.002 TYR M 667 PHE 0.021 0.001 PHE P 486 TRP 0.030 0.001 TRP B 28 HIS 0.008 0.001 HIS N 649 Details of bonding type rmsd covalent geometry : bond 0.00314 (39017) covalent geometry : angle 0.65354 (52843) hydrogen bonds : bond 0.04200 ( 1878) hydrogen bonds : angle 4.58239 ( 5439) Misc. bond : bond 0.00039 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.25 seconds wall clock time: 81 minutes 0.76 seconds (4860.76 seconds total)