Starting phenix.real_space_refine on Tue Apr 9 18:32:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/04_2024/8eex_28064.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 36 5.49 5 S 76 5.16 5 C 10671 2.51 5 N 3010 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "A GLU 1501": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A GLU 1577": "OE1" <-> "OE2" Residue "A GLU 1587": "OE1" <-> "OE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 667": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1284, 10305 Classifications: {'peptide': 1284} Link IDs: {'CIS': 1, 'PTRANS': 72, 'TRANS': 1210} Chain breaks: 5 Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 6011 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 697} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 762 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 9, 'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 14} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 704 SG CYS A 86 89.905 116.535 91.991 1.00 74.83 S ATOM 950 SG CYS A 115 92.236 116.569 94.788 1.00 87.00 S ATOM 1012 SG CYS A 123 88.236 115.548 95.077 1.00 73.92 S ATOM 1036 SG CYS A 126 90.734 113.241 93.622 1.00 63.99 S ATOM 3426 SG CYS A 463 74.133 104.568 62.647 1.00 67.26 S ATOM 3502 SG CYS A 474 74.849 106.990 64.682 1.00 34.89 S ATOM 3524 SG CYS A 477 75.549 104.465 66.866 1.00 40.87 S ATOM 5342 SG CYS A 706 70.169 86.104 40.168 1.00 72.83 S ATOM 5357 SG CYS A 708 66.598 86.781 39.623 1.00 53.83 S ATOM 5379 SG CYS A 711 67.973 86.372 43.191 1.00 57.94 S ATOM 7408 SG CYS A 965 52.456 52.410 30.345 1.00 46.61 S ATOM 7968 SG CYS A1312 55.769 54.200 30.125 1.00 41.93 S ATOM 8207 SG CYS A1342 52.853 55.203 27.921 1.00 44.26 S ATOM 8225 SG CYS A1345 52.993 56.145 31.600 1.00 51.97 S Time building chain proxies: 9.42, per 1000 atoms: 0.55 Number of scatterers: 17082 At special positions: 0 Unit cell: (133.263, 155.142, 121.329, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 76 16.00 P 36 15.00 O 3285 8.00 N 3010 7.00 C 10671 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 86 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 126 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 123 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 115 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 463 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 474 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 477 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 706 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 708 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 711 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1312 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1342 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 965 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1345 " Number of angles added : 15 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 43.5% alpha, 17.8% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.578A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.684A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 302 removed outlier: 5.411A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.543A pdb=" N LYS A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.710A pdb=" N ILE A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.522A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 removed outlier: 3.592A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.605A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.535A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1335 removed outlier: 3.877A pdb=" N LEU A1334 " --> pdb=" O GLU A1330 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1330 through 1335' Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.052A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 removed outlier: 4.019A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 4.792A pdb=" N GLN A1590 " --> pdb=" O LYS A1586 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS A1591 " --> pdb=" O GLU A1587 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.688A pdb=" N GLN B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 79 through 85 removed outlier: 4.147A pdb=" N TYR B 84 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 removed outlier: 4.717A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 3.546A pdb=" N LEU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.613A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.532A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 277 through 293 removed outlier: 4.421A pdb=" N ASP B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 removed outlier: 4.448A pdb=" N GLU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 360 through 374 removed outlier: 3.715A pdb=" N ASN B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 4.004A pdb=" N ASN B 391 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 464 through 482 Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.754A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.599A pdb=" N ASN B 585 " --> pdb=" O GLN B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 656 through 662 removed outlier: 4.506A pdb=" N SER B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 683 Processing helix chain 'B' and resid 696 through 710 Processing helix chain 'B' and resid 712 through 732 removed outlier: 3.773A pdb=" N GLN B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 731 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.717A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.204A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 46 removed outlier: 7.935A pdb=" N LYS A 51 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.300A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.920A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.920A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 501 Processing sheet with id=AB1, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.824A pdb=" N THR A 510 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.031A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.031A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 692 through 693 removed outlier: 3.588A pdb=" N VAL A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.610A pdb=" N ILE A 943 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 5.507A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.574A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 936 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.858A pdb=" N TYR B 321 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU B 359 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER B 323 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 457 through 462 removed outlier: 6.527A pdb=" N ILE B 424 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 518 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 426 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 532 through 533 Processing sheet with id=AC5, first strand: chain 'B' and resid 589 through 591 removed outlier: 6.414A pdb=" N LEU B 610 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY B 691 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 616 through 617 730 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2821 1.27 - 1.41: 4474 1.41 - 1.55: 10020 1.55 - 1.69: 109 1.69 - 1.83: 114 Bond restraints: 17538 Sorted by residual: bond pdb=" CG PRO A1249 " pdb=" CD PRO A1249 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" N PRO A1249 " pdb=" CD PRO A1249 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" CB LYS A 47 " pdb=" CG LYS A 47 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.84e+00 bond pdb=" N ASN B 3 " pdb=" CA ASN B 3 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.70e+00 bond pdb=" C ALA B 741 " pdb=" N PRO B 742 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.60e+00 ... (remaining 17533 not shown) Histogram of bond angle deviations from ideal: 83.48 - 95.46: 2 95.46 - 107.44: 897 107.44 - 119.42: 14172 119.42 - 131.41: 8677 131.41 - 143.39: 56 Bond angle restraints: 23804 Sorted by residual: angle pdb=" N PRO A1249 " pdb=" CD PRO A1249 " pdb=" CG PRO A1249 " ideal model delta sigma weight residual 103.20 83.48 19.72 1.50e+00 4.44e-01 1.73e+02 angle pdb=" C ARG A1558 " pdb=" N VAL A1559 " pdb=" CA VAL A1559 " ideal model delta sigma weight residual 121.70 143.39 -21.69 1.80e+00 3.09e-01 1.45e+02 angle pdb=" CA PRO A1249 " pdb=" CB PRO A1249 " pdb=" CG PRO A1249 " ideal model delta sigma weight residual 104.50 89.36 15.14 1.90e+00 2.77e-01 6.35e+01 angle pdb=" CA PRO A1249 " pdb=" N PRO A1249 " pdb=" CD PRO A1249 " ideal model delta sigma weight residual 112.00 105.68 6.32 1.40e+00 5.10e-01 2.04e+01 angle pdb=" C GLU A1518 " pdb=" N ILE A1519 " pdb=" CA ILE A1519 " ideal model delta sigma weight residual 120.24 122.93 -2.69 6.30e-01 2.52e+00 1.83e+01 ... (remaining 23799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 10353 35.49 - 70.98: 333 70.98 - 106.47: 32 106.47 - 141.96: 1 141.96 - 177.45: 6 Dihedral angle restraints: 10725 sinusoidal: 4897 harmonic: 5828 Sorted by residual: dihedral pdb=" O4' C C -8 " pdb=" C1' C C -8 " pdb=" N1 C C -8 " pdb=" C2 C C -8 " ideal model delta sinusoidal sigma weight residual -160.00 17.25 -177.25 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 6.81 -166.81 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -160.00 2.46 -162.46 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 10722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2112 0.062 - 0.124: 363 0.124 - 0.186: 39 0.186 - 0.248: 4 0.248 - 0.310: 1 Chirality restraints: 2519 Sorted by residual: chirality pdb=" CA VAL A1559 " pdb=" N VAL A1559 " pdb=" C VAL A1559 " pdb=" CB VAL A1559 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' U C 11 " pdb=" O4' U C 11 " pdb=" C2' U C 11 " pdb=" N1 U C 11 " both_signs ideal model delta sigma weight residual False 2.45 2.23 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2516 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 102 " 0.474 9.50e-02 1.11e+02 2.12e-01 2.80e+01 pdb=" NE ARG A 102 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 102 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 102 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 102 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1248 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A1249 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A1249 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A1249 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1376 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO A1377 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.044 5.00e-02 4.00e+02 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 556 2.72 - 3.26: 16635 3.26 - 3.81: 26178 3.81 - 4.35: 36153 4.35 - 4.90: 59118 Nonbonded interactions: 138640 Sorted by model distance: nonbonded pdb=" OD2 ASP A 177 " pdb=" OG SER A 180 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASP B 117 " pdb=" N ASP B 118 " model vdw 2.177 2.520 nonbonded pdb=" O SER A 81 " pdb=" OG SER A 81 " model vdw 2.212 2.440 nonbonded pdb=" N GLU A 707 " pdb=" OE1 GLU A 707 " model vdw 2.223 2.520 nonbonded pdb=" N GLU B 169 " pdb=" OE1 GLU B 169 " model vdw 2.247 2.520 ... (remaining 138635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.060 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 56.270 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.006 0.371 17538 Z= 0.349 Angle : 0.888 21.689 23804 Z= 0.470 Chirality : 0.047 0.310 2519 Planarity : 0.011 0.212 2980 Dihedral : 16.997 177.449 6955 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.51 % Allowed : 12.46 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 1990 helix: -0.61 (0.18), residues: 730 sheet: 0.46 (0.27), residues: 283 loop : -0.08 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 544 HIS 0.008 0.001 HIS A 887 PHE 0.032 0.002 PHE B 197 TYR 0.025 0.002 TYR B 209 ARG 0.018 0.001 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 319 time to evaluate : 1.906 Fit side-chains REVERT: A 47 LYS cc_start: 0.7548 (tptt) cc_final: 0.6943 (ttmm) REVERT: A 199 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7640 (mtp180) REVERT: A 227 ARG cc_start: 0.8924 (mtm-85) cc_final: 0.8716 (mtt-85) REVERT: A 422 ASP cc_start: 0.7087 (t0) cc_final: 0.6818 (t0) REVERT: A 460 ASP cc_start: 0.8626 (t0) cc_final: 0.8029 (t0) REVERT: A 524 GLU cc_start: 0.8719 (pt0) cc_final: 0.8311 (pm20) REVERT: A 587 GLN cc_start: 0.8421 (mt0) cc_final: 0.7848 (mm-40) REVERT: A 669 LYS cc_start: 0.7092 (mttt) cc_final: 0.6808 (mmmt) REVERT: A 1291 ARG cc_start: 0.7303 (tpt170) cc_final: 0.6143 (tpm170) REVERT: A 1581 ASP cc_start: 0.7814 (m-30) cc_final: 0.7038 (t70) REVERT: B 16 LYS cc_start: 0.6280 (mttt) cc_final: 0.5979 (pttm) REVERT: B 22 ASP cc_start: 0.7547 (m-30) cc_final: 0.7247 (m-30) REVERT: B 199 LEU cc_start: 0.7401 (tp) cc_final: 0.7037 (tp) REVERT: B 249 ARG cc_start: 0.6144 (mtp85) cc_final: 0.5529 (ttp-110) REVERT: B 387 ILE cc_start: 0.8160 (tt) cc_final: 0.7856 (tp) REVERT: B 667 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6586 (mp0) REVERT: B 737 PHE cc_start: 0.7763 (t80) cc_final: 0.7541 (t80) outliers start: 9 outliers final: 2 residues processed: 322 average time/residue: 1.7220 time to fit residues: 607.3176 Evaluate side-chains 174 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 841 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 611 ASN A 626 HIS A 640 ASN A 834 ASN B 36 GLN B 372 HIS B 391 ASN B 606 ASN B 683 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17538 Z= 0.328 Angle : 0.683 12.500 23804 Z= 0.359 Chirality : 0.047 0.287 2519 Planarity : 0.006 0.066 2980 Dihedral : 14.671 176.578 2780 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.32 % Allowed : 14.18 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 1990 helix: 0.39 (0.19), residues: 736 sheet: 0.50 (0.27), residues: 288 loop : -0.21 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.031 0.002 PHE B 713 TYR 0.015 0.002 TYR A1328 ARG 0.010 0.001 ARG B 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 2.067 Fit side-chains REVERT: A 227 ARG cc_start: 0.9057 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: A 387 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: A 401 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (tp) REVERT: A 422 ASP cc_start: 0.7107 (t0) cc_final: 0.6809 (t0) REVERT: A 497 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 524 GLU cc_start: 0.8759 (pt0) cc_final: 0.8305 (pm20) REVERT: A 587 GLN cc_start: 0.8494 (mt0) cc_final: 0.7908 (mm-40) REVERT: A 667 GLU cc_start: 0.7635 (tt0) cc_final: 0.7416 (mt-10) REVERT: A 669 LYS cc_start: 0.7087 (mttt) cc_final: 0.6647 (mmmt) REVERT: A 758 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: A 816 GLN cc_start: 0.8396 (mt0) cc_final: 0.7664 (mm110) REVERT: A 896 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7923 (mtp85) REVERT: A 917 ARG cc_start: 0.6735 (ttt-90) cc_final: 0.6481 (ttt-90) REVERT: A 1286 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: A 1319 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7059 (m-30) REVERT: A 1444 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8678 (m) REVERT: A 1592 LYS cc_start: 0.8809 (mmpt) cc_final: 0.8553 (mmtm) REVERT: B 16 LYS cc_start: 0.6398 (mttt) cc_final: 0.5984 (pttm) REVERT: B 18 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5737 (p0) REVERT: B 60 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 109 ASN cc_start: 0.7035 (t0) cc_final: 0.6832 (m-40) REVERT: B 118 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6849 (t0) REVERT: B 380 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 383 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6468 (pt) REVERT: B 607 PRO cc_start: 0.5128 (Cg_exo) cc_final: 0.4851 (Cg_endo) REVERT: B 662 MET cc_start: 0.7775 (mtp) cc_final: 0.7001 (ttm) REVERT: B 667 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6688 (mp0) outliers start: 58 outliers final: 12 residues processed: 231 average time/residue: 1.7107 time to fit residues: 432.4107 Evaluate side-chains 175 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1319 ASP Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 125 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 40.0000 chunk 199 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 834 ASN A1442 ASN A1573 ASN B 556 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17538 Z= 0.286 Angle : 0.622 11.975 23804 Z= 0.324 Chirality : 0.045 0.281 2519 Planarity : 0.005 0.069 2980 Dihedral : 14.521 175.778 2776 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.77 % Allowed : 15.78 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 1990 helix: 0.84 (0.19), residues: 733 sheet: 0.38 (0.27), residues: 300 loop : -0.21 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 457 HIS 0.006 0.001 HIS A1483 PHE 0.019 0.002 PHE B 737 TYR 0.015 0.001 TYR A 492 ARG 0.007 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 164 time to evaluate : 1.951 Fit side-chains REVERT: A 47 LYS cc_start: 0.7374 (tptt) cc_final: 0.7035 (ttmm) REVERT: A 86 CYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 147 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7460 (tpp80) REVERT: A 227 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.7509 (mtm-85) REVERT: A 387 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: A 401 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 422 ASP cc_start: 0.7053 (t0) cc_final: 0.6790 (t0) REVERT: A 497 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: A 524 GLU cc_start: 0.8763 (pt0) cc_final: 0.8243 (pm20) REVERT: A 587 GLN cc_start: 0.8479 (mt0) cc_final: 0.7900 (mm-40) REVERT: A 667 GLU cc_start: 0.7590 (tt0) cc_final: 0.7329 (mt-10) REVERT: A 669 LYS cc_start: 0.7049 (mttt) cc_final: 0.6647 (mmmt) REVERT: A 758 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 816 GLN cc_start: 0.8404 (mt0) cc_final: 0.7634 (mm110) REVERT: A 917 ARG cc_start: 0.6689 (ttt-90) cc_final: 0.6480 (ttt-90) REVERT: A 1243 ARG cc_start: 0.7979 (tmm-80) cc_final: 0.7640 (ttp80) REVERT: A 1286 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5718 (m-30) REVERT: A 1299 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7382 (mtm-85) REVERT: A 1592 LYS cc_start: 0.8914 (mmpt) cc_final: 0.8545 (mmtm) REVERT: B 16 LYS cc_start: 0.6648 (mttt) cc_final: 0.6251 (pttm) REVERT: B 18 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5624 (p0) REVERT: B 60 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8090 (mt) REVERT: B 118 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6890 (t0) REVERT: B 138 LYS cc_start: 0.7428 (tppp) cc_final: 0.7223 (mmtt) REVERT: B 380 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6966 (mm-30) REVERT: B 383 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6364 (pt) REVERT: B 607 PRO cc_start: 0.4999 (Cg_exo) cc_final: 0.4718 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6695 (mp0) outliers start: 66 outliers final: 26 residues processed: 210 average time/residue: 1.6421 time to fit residues: 378.8034 Evaluate side-chains 190 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 834 ASN A1442 ASN B 109 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 17538 Z= 0.644 Angle : 0.791 15.043 23804 Z= 0.408 Chirality : 0.055 0.343 2519 Planarity : 0.007 0.068 2980 Dihedral : 14.702 176.653 2776 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.86 % Allowed : 16.07 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 1990 helix: 0.42 (0.19), residues: 733 sheet: 0.19 (0.27), residues: 292 loop : -0.68 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1549 HIS 0.009 0.002 HIS B 556 PHE 0.025 0.003 PHE A 776 TYR 0.022 0.002 TYR A 492 ARG 0.007 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 168 time to evaluate : 2.071 Fit side-chains REVERT: A 19 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7610 (mtpp) REVERT: A 47 LYS cc_start: 0.7568 (tptt) cc_final: 0.7287 (ttmm) REVERT: A 147 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7446 (tpp80) REVERT: A 297 LYS cc_start: 0.8144 (mptt) cc_final: 0.7913 (mmmt) REVERT: A 387 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: A 401 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8586 (tm) REVERT: A 497 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: A 587 GLN cc_start: 0.8543 (mt0) cc_final: 0.8339 (tt0) REVERT: A 740 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: A 758 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: A 780 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: A 1286 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5739 (m-30) REVERT: A 1299 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7658 (mtm-85) REVERT: A 1444 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8823 (m) REVERT: A 1581 ASP cc_start: 0.8119 (m-30) cc_final: 0.7099 (t0) REVERT: A 1592 LYS cc_start: 0.8882 (mmpt) cc_final: 0.8510 (mmtm) REVERT: B 16 LYS cc_start: 0.6918 (mttt) cc_final: 0.6494 (pttm) REVERT: B 118 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6957 (t0) REVERT: B 138 LYS cc_start: 0.7952 (tppp) cc_final: 0.7365 (mmtt) REVERT: B 204 PHE cc_start: 0.4866 (p90) cc_final: 0.4265 (t80) REVERT: B 383 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6187 (pt) REVERT: B 607 PRO cc_start: 0.4826 (Cg_exo) cc_final: 0.4552 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6750 (mp0) outliers start: 85 outliers final: 37 residues processed: 230 average time/residue: 1.6333 time to fit residues: 412.9769 Evaluate side-chains 206 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 7.9990 chunk 111 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A1442 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17538 Z= 0.205 Angle : 0.569 10.900 23804 Z= 0.296 Chirality : 0.042 0.238 2519 Planarity : 0.005 0.057 2980 Dihedral : 14.472 173.488 2776 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.49 % Allowed : 17.78 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 1990 helix: 1.02 (0.19), residues: 733 sheet: 0.29 (0.27), residues: 296 loop : -0.42 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.016 0.001 PHE A 757 TYR 0.013 0.001 TYR A 492 ARG 0.009 0.000 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.853 Fit side-chains REVERT: A 147 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7253 (tpp80) REVERT: A 297 LYS cc_start: 0.8081 (mptt) cc_final: 0.7856 (mmmt) REVERT: A 387 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 401 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8743 (tp) REVERT: A 497 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: A 524 GLU cc_start: 0.8762 (pt0) cc_final: 0.8242 (pm20) REVERT: A 559 MET cc_start: 0.9314 (mmm) cc_final: 0.8886 (mtm) REVERT: A 758 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: A 780 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: A 849 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8168 (ttpp) REVERT: A 1236 ILE cc_start: 0.8044 (mt) cc_final: 0.7672 (pt) REVERT: A 1286 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5694 (m-30) REVERT: A 1299 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7549 (ptt-90) REVERT: A 1300 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: A 1444 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 1581 ASP cc_start: 0.7920 (m-30) cc_final: 0.7056 (t0) REVERT: A 1592 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8487 (mmtm) REVERT: B 118 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6992 (t0) REVERT: B 138 LYS cc_start: 0.7877 (tppp) cc_final: 0.7321 (mmtt) REVERT: B 237 ARG cc_start: 0.3937 (OUTLIER) cc_final: 0.3536 (mmm160) REVERT: B 380 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6361 (mm-30) REVERT: B 383 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6377 (pt) REVERT: B 454 LYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4717 (mtpt) REVERT: B 607 PRO cc_start: 0.5007 (Cg_exo) cc_final: 0.4713 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6692 (mp0) outliers start: 61 outliers final: 17 residues processed: 210 average time/residue: 1.6601 time to fit residues: 382.5343 Evaluate side-chains 180 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.0060 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A1442 ASN B 234 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17538 Z= 0.356 Angle : 0.624 10.891 23804 Z= 0.321 Chirality : 0.046 0.240 2519 Planarity : 0.005 0.059 2980 Dihedral : 14.500 175.154 2776 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.00 % Allowed : 18.18 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 1990 helix: 0.97 (0.19), residues: 733 sheet: 0.26 (0.27), residues: 296 loop : -0.51 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 457 HIS 0.006 0.001 HIS A1483 PHE 0.019 0.002 PHE A 776 TYR 0.016 0.001 TYR A 492 ARG 0.006 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 158 time to evaluate : 2.383 Fit side-chains REVERT: A 147 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7282 (tpp80) REVERT: A 297 LYS cc_start: 0.8118 (mptt) cc_final: 0.7879 (mmmt) REVERT: A 387 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: A 401 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8761 (tp) REVERT: A 497 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: A 740 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: A 758 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: A 780 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7688 (ttm-80) REVERT: A 849 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8200 (ttpp) REVERT: A 855 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7364 (mmt180) REVERT: A 1236 ILE cc_start: 0.8048 (mt) cc_final: 0.7675 (pt) REVERT: A 1286 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.5747 (m-30) REVERT: A 1299 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7643 (ptt-90) REVERT: A 1393 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7338 (ptm160) REVERT: A 1444 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 1581 ASP cc_start: 0.8085 (m-30) cc_final: 0.7130 (t0) REVERT: A 1592 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8494 (mmtm) REVERT: B 118 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7047 (t0) REVERT: B 138 LYS cc_start: 0.7933 (tppp) cc_final: 0.7292 (mmtt) REVERT: B 242 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6333 (pt0) REVERT: B 380 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6398 (mm-30) REVERT: B 383 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6283 (pt) REVERT: B 454 LYS cc_start: 0.5019 (OUTLIER) cc_final: 0.4736 (mtpt) REVERT: B 607 PRO cc_start: 0.4897 (Cg_exo) cc_final: 0.4628 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6735 (mp0) outliers start: 70 outliers final: 31 residues processed: 206 average time/residue: 1.5867 time to fit residues: 360.4105 Evaluate side-chains 196 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 531 GLN A1442 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17538 Z= 0.202 Angle : 0.552 9.417 23804 Z= 0.285 Chirality : 0.042 0.217 2519 Planarity : 0.004 0.060 2980 Dihedral : 14.406 174.130 2776 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.26 % Allowed : 19.04 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 1990 helix: 1.27 (0.19), residues: 732 sheet: 0.28 (0.28), residues: 292 loop : -0.36 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 457 HIS 0.005 0.001 HIS A1483 PHE 0.015 0.001 PHE A 757 TYR 0.012 0.001 TYR A 492 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 1.842 Fit side-chains REVERT: A 147 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7186 (tpp80) REVERT: A 297 LYS cc_start: 0.8092 (mptt) cc_final: 0.7846 (mmmt) REVERT: A 387 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: A 401 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8792 (tp) REVERT: A 497 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 559 MET cc_start: 0.9275 (mmm) cc_final: 0.8920 (mtm) REVERT: A 780 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: A 849 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (ttpp) REVERT: A 1236 ILE cc_start: 0.8037 (mt) cc_final: 0.7672 (pt) REVERT: A 1286 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5703 (m-30) REVERT: A 1299 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7612 (ptt-90) REVERT: A 1393 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7395 (ptm160) REVERT: A 1444 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8711 (m) REVERT: A 1581 ASP cc_start: 0.7941 (m-30) cc_final: 0.7117 (t0) REVERT: A 1592 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8487 (mmtm) REVERT: B 138 LYS cc_start: 0.7895 (tppp) cc_final: 0.7188 (mmtt) REVERT: B 233 GLU cc_start: 0.5342 (tp30) cc_final: 0.4545 (mm-30) REVERT: B 242 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6328 (pt0) REVERT: B 380 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6452 (mm-30) REVERT: B 383 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6384 (pt) REVERT: B 454 LYS cc_start: 0.4978 (OUTLIER) cc_final: 0.4698 (mtpt) REVERT: B 607 PRO cc_start: 0.5058 (Cg_exo) cc_final: 0.4769 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6744 (mp0) REVERT: B 722 MET cc_start: 0.6699 (mmm) cc_final: 0.6434 (tpt) outliers start: 57 outliers final: 25 residues processed: 201 average time/residue: 1.7032 time to fit residues: 374.9337 Evaluate side-chains 186 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 96 optimal weight: 0.0470 chunk 18 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17538 Z= 0.136 Angle : 0.508 8.742 23804 Z= 0.263 Chirality : 0.040 0.200 2519 Planarity : 0.004 0.054 2980 Dihedral : 14.298 173.951 2776 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.94 % Allowed : 20.53 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1990 helix: 1.66 (0.20), residues: 720 sheet: 0.32 (0.28), residues: 299 loop : -0.22 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 457 HIS 0.004 0.001 HIS A1483 PHE 0.012 0.001 PHE A 757 TYR 0.009 0.001 TYR A 492 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 2.115 Fit side-chains REVERT: A 309 LYS cc_start: 0.7769 (mmtp) cc_final: 0.6625 (mmtm) REVERT: A 497 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: A 1236 ILE cc_start: 0.7967 (mt) cc_final: 0.7590 (pt) REVERT: A 1299 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7665 (ptt-90) REVERT: A 1393 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7349 (ptm160) REVERT: A 1592 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8477 (mmtm) REVERT: B 138 LYS cc_start: 0.7864 (tppp) cc_final: 0.7266 (mmtt) REVERT: B 233 GLU cc_start: 0.5505 (tp30) cc_final: 0.4584 (mm-30) REVERT: B 380 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6661 (mm-30) REVERT: B 390 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6484 (mm-30) REVERT: B 394 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6614 (ttp-110) REVERT: B 454 LYS cc_start: 0.4946 (OUTLIER) cc_final: 0.4693 (mtpt) REVERT: B 607 PRO cc_start: 0.5142 (Cg_exo) cc_final: 0.4853 (Cg_endo) REVERT: B 667 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6710 (mp0) outliers start: 34 outliers final: 13 residues processed: 196 average time/residue: 1.7048 time to fit residues: 366.5162 Evaluate side-chains 169 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 181 optimal weight: 0.0170 chunk 119 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 619 ASN B 36 GLN B 256 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17538 Z= 0.287 Angle : 0.586 9.936 23804 Z= 0.302 Chirality : 0.044 0.221 2519 Planarity : 0.005 0.056 2980 Dihedral : 14.376 175.376 2776 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.52 % Allowed : 20.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1990 helix: 1.49 (0.19), residues: 720 sheet: 0.28 (0.28), residues: 294 loop : -0.32 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 457 HIS 0.004 0.001 HIS A1483 PHE 0.019 0.002 PHE A 776 TYR 0.015 0.001 TYR A 492 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 2.089 Fit side-chains REVERT: A 147 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7133 (tpp80) REVERT: A 387 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: A 401 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 497 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 705 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: A 1236 ILE cc_start: 0.8041 (mt) cc_final: 0.7669 (pt) REVERT: A 1299 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7662 (ptt-90) REVERT: A 1393 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: A 1444 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8769 (m) REVERT: A 1581 ASP cc_start: 0.7976 (m-30) cc_final: 0.7125 (t0) REVERT: A 1592 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8478 (mmtm) REVERT: B 204 PHE cc_start: 0.4830 (p90) cc_final: 0.4629 (t80) REVERT: B 237 ARG cc_start: 0.3729 (mtp180) cc_final: 0.3279 (mtp85) REVERT: B 380 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6627 (mm-30) REVERT: B 454 LYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4708 (mtpt) REVERT: B 458 GLN cc_start: 0.6578 (mt0) cc_final: 0.6369 (pt0) REVERT: B 607 PRO cc_start: 0.5083 (Cg_exo) cc_final: 0.4798 (Cg_endo) REVERT: B 648 LEU cc_start: 0.6407 (mt) cc_final: 0.6125 (mp) REVERT: B 667 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6746 (mp0) outliers start: 44 outliers final: 20 residues processed: 184 average time/residue: 1.6945 time to fit residues: 342.0991 Evaluate side-chains 175 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN B 36 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17538 Z= 0.280 Angle : 0.583 9.728 23804 Z= 0.301 Chirality : 0.044 0.224 2519 Planarity : 0.005 0.055 2980 Dihedral : 14.366 174.745 2776 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.83 % Allowed : 21.27 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 1990 helix: 1.38 (0.19), residues: 725 sheet: 0.21 (0.28), residues: 294 loop : -0.39 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 324 HIS 0.006 0.001 HIS A1483 PHE 0.017 0.002 PHE A 776 TYR 0.014 0.001 TYR A 492 ARG 0.012 0.001 ARG B 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7110 (tpp80) REVERT: A 387 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 401 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8832 (tp) REVERT: A 497 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: A 849 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8175 (ttpp) REVERT: A 1236 ILE cc_start: 0.8006 (mt) cc_final: 0.7631 (pt) REVERT: A 1299 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7690 (ptt-90) REVERT: A 1393 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7462 (ptm160) REVERT: A 1444 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8774 (m) REVERT: A 1581 ASP cc_start: 0.8055 (m-30) cc_final: 0.7125 (t0) REVERT: A 1592 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8486 (mmtm) REVERT: B 212 ARG cc_start: 0.6709 (ttp80) cc_final: 0.6458 (tpt90) REVERT: B 233 GLU cc_start: 0.5211 (tp30) cc_final: 0.4703 (mm-30) REVERT: B 237 ARG cc_start: 0.3738 (mtp180) cc_final: 0.3365 (mtp85) REVERT: B 380 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 383 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6446 (pt) REVERT: B 454 LYS cc_start: 0.4973 (OUTLIER) cc_final: 0.4695 (mtpt) REVERT: B 607 PRO cc_start: 0.5118 (Cg_exo) cc_final: 0.4827 (Cg_endo) REVERT: B 648 LEU cc_start: 0.6410 (mt) cc_final: 0.6123 (mp) REVERT: B 667 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6762 (mp0) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 1.7068 time to fit residues: 327.8580 Evaluate side-chains 172 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 688 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** B 389 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 = 0.3753 r_free = 0.3753 target = 0.150903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110901 restraints weight = 20950.668| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.05 r_work: 0.2621 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17538 Z= 0.221 Angle : 0.562 9.390 23804 Z= 0.290 Chirality : 0.042 0.212 2519 Planarity : 0.004 0.054 2980 Dihedral : 14.335 174.381 2776 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.94 % Allowed : 21.21 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1990 helix: 1.50 (0.20), residues: 720 sheet: 0.22 (0.28), residues: 294 loop : -0.32 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 324 HIS 0.005 0.001 HIS A1483 PHE 0.017 0.001 PHE B 204 TYR 0.013 0.001 TYR A 492 ARG 0.010 0.000 ARG B 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6375.94 seconds wall clock time: 115 minutes 14.63 seconds (6914.63 seconds total)