Starting phenix.real_space_refine (version: dev) on Tue Dec 13 20:35:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/12_2022/8eex_28064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/12_2022/8eex_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_28064/12_2022/8eex_28064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/12_2022/8eex_28064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/12_2022/8eex_28064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eex_28064/12_2022/8eex_28064.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 9.65, per 1000 atoms: 0.56 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: 6.92 Conformation dependent library (CDL) restraints added in 2.3 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: 4.82 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: 7.32 Time building geometry restraints manager: 7.42 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=" 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=" C ARG A1558 " pdb=" N VAL A1559 " pdb=" CA VAL A1559 " ideal model delta sigma weight residual 123.00 143.39 -20.39 3.00e+00 1.11e-01 4.62e+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: 10274 35.49 - 70.98: 279 70.98 - 106.47: 25 106.47 - 141.96: 1 141.96 - 177.45: 6 Dihedral angle restraints: 10585 sinusoidal: 4757 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 10582 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 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. 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: 1.850 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: 8.490 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 52.900 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.887 20.389 23804 Z= 0.466 Chirality : 0.047 0.310 2519 Planarity : 0.011 0.212 2980 Dihedral : 16.121 177.449 6815 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.51 % 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 *********************** 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 : 2.269 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 322 average time/residue: 1.5038 time to fit residues: 532.7252 Evaluate side-chains 163 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2179 time to fit residues: 3.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 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: 0.8326 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 17538 Z= 0.328 Angle : 0.696 23.032 23804 Z= 0.361 Chirality : 0.047 0.229 2519 Planarity : 0.006 0.068 2980 Dihedral : 11.717 176.492 2636 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 3.49 % 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: 0.12 (0.18), residues: 1990 helix: 0.40 (0.19), residues: 736 sheet: 0.50 (0.27), residues: 288 loop : -0.18 (0.20), residues: 966 *********************** 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 247 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 186 time to evaluate : 2.083 Fit side-chains outliers start: 61 outliers final: 15 residues processed: 222 average time/residue: 1.4616 time to fit residues: 358.6110 Evaluate side-chains 160 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.2164 time to fit residues: 4.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 153 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 184 optimal weight: 40.0000 chunk 199 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 148 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 816 GLN A 834 ASN A1442 ASN A1573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 17538 Z= 0.267 Angle : 0.620 21.837 23804 Z= 0.318 Chirality : 0.044 0.219 2519 Planarity : 0.005 0.066 2980 Dihedral : 11.514 174.948 2636 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 3.32 % 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: 0.39 (0.18), residues: 1990 helix: 0.87 (0.19), residues: 733 sheet: 0.40 (0.27), residues: 296 loop : -0.16 (0.20), residues: 961 *********************** 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 221 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 163 time to evaluate : 2.124 Fit side-chains outliers start: 58 outliers final: 27 residues processed: 203 average time/residue: 1.4726 time to fit residues: 331.6936 Evaluate side-chains 173 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.5877 time to fit residues: 8.6231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 816 GLN A 834 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.075 17538 Z= 0.582 Angle : 0.769 27.243 23804 Z= 0.390 Chirality : 0.052 0.277 2519 Planarity : 0.006 0.058 2980 Dihedral : 11.720 175.759 2636 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 4.29 % 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: -0.11 (0.18), residues: 1990 helix: 0.55 (0.19), residues: 733 sheet: 0.13 (0.27), residues: 302 loop : -0.54 (0.19), residues: 955 *********************** 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 240 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 165 time to evaluate : 2.006 Fit side-chains outliers start: 75 outliers final: 38 residues processed: 221 average time/residue: 1.4906 time to fit residues: 364.4846 Evaluate side-chains 192 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 7 average time/residue: 0.5030 time to fit residues: 7.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 80 optimal weight: 0.2980 chunk 167 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN 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: 0.8326 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17538 Z= 0.187 Angle : 0.567 19.917 23804 Z= 0.289 Chirality : 0.042 0.217 2519 Planarity : 0.005 0.058 2980 Dihedral : 11.385 173.026 2636 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 3.03 % 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: 0.39 (0.18), residues: 1990 helix: 1.14 (0.19), residues: 727 sheet: 0.30 (0.28), residues: 291 loop : -0.37 (0.19), residues: 972 *********************** 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 217 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 2.169 Fit side-chains outliers start: 53 outliers final: 25 residues processed: 203 average time/residue: 1.5446 time to fit residues: 347.9718 Evaluate side-chains 170 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.2535 time to fit residues: 4.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.0980 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN ** 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: 0.8354 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 17538 Z= 0.334 Angle : 0.630 23.078 23804 Z= 0.317 Chirality : 0.045 0.231 2519 Planarity : 0.005 0.059 2980 Dihedral : 11.438 174.944 2636 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 3.83 % 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: 0.31 (0.18), residues: 1990 helix: 1.15 (0.19), residues: 721 sheet: 0.25 (0.27), residues: 296 loop : -0.48 (0.19), residues: 973 *********************** 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 221 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 154 time to evaluate : 2.228 Fit side-chains outliers start: 67 outliers final: 35 residues processed: 205 average time/residue: 1.5016 time to fit residues: 341.2817 Evaluate side-chains 186 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 0.5085 time to fit residues: 7.3607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** 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: 0.8327 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17538 Z= 0.194 Angle : 0.563 20.194 23804 Z= 0.285 Chirality : 0.042 0.209 2519 Planarity : 0.004 0.059 2980 Dihedral : 11.303 173.759 2636 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.97 % 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: 0.53 (0.18), residues: 1990 helix: 1.41 (0.19), residues: 720 sheet: 0.33 (0.28), residues: 290 loop : -0.38 (0.19), residues: 980 *********************** 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 215 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 2.079 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 203 average time/residue: 1.4720 time to fit residues: 331.2091 Evaluate side-chains 178 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.2711 time to fit residues: 3.9698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.0000 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8346 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17538 Z= 0.291 Angle : 0.606 22.145 23804 Z= 0.307 Chirality : 0.044 0.219 2519 Planarity : 0.005 0.059 2980 Dihedral : 11.342 174.710 2636 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 2.74 % 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: 1.30 (0.19), residues: 720 sheet: 0.20 (0.28), residues: 293 loop : -0.39 (0.19), residues: 977 *********************** 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 205 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 2.027 Fit side-chains outliers start: 48 outliers final: 32 residues processed: 192 average time/residue: 1.4695 time to fit residues: 314.1275 Evaluate side-chains 177 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.7404 time to fit residues: 6.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 chunk 164 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 721 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17538 Z= 0.227 Angle : 0.579 20.780 23804 Z= 0.292 Chirality : 0.043 0.324 2519 Planarity : 0.004 0.060 2980 Dihedral : 11.268 174.198 2636 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.29 % 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: 0.52 (0.18), residues: 1990 helix: 1.41 (0.19), residues: 719 sheet: 0.20 (0.28), residues: 294 loop : -0.35 (0.19), residues: 977 *********************** 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 193 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 2.143 Fit side-chains outliers start: 40 outliers final: 30 residues processed: 186 average time/residue: 1.4546 time to fit residues: 300.8653 Evaluate side-chains 180 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.2365 time to fit residues: 3.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN A1442 ASN B 253 HIS ** 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: 0.8353 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 17538 Z= 0.345 Angle : 0.635 23.124 23804 Z= 0.321 Chirality : 0.046 0.244 2519 Planarity : 0.005 0.061 2980 Dihedral : 11.361 175.124 2636 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.83 % 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: 1.15 (0.19), residues: 725 sheet: 0.13 (0.28), residues: 293 loop : -0.47 (0.19), residues: 972 ********************** 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 : 2.202 Fit side-chains outliers start: 32 outliers final: 30 residues processed: 181 average time/residue: 1.5070 time to fit residues: 302.5067 Evaluate side-chains 174 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.2905 time to fit residues: 4.1890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 23 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 816 GLN A1442 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108924 restraints weight = 21025.927| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.61 r_work: 0.2644 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3539 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= 0.176 Angle : 0.558 19.966 23804 Z= 0.284 Chirality : 0.042 0.199 2519 Planarity : 0.004 0.057 2980 Dihedral : 11.216 173.429 2636 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.72 % 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: 0.55 (0.19), residues: 1990 helix: 1.44 (0.20), residues: 720 sheet: 0.16 (0.28), residues: 294 loop : -0.33 (0.20), residues: 976 =============================================================================== Job complete usr+sys time: 5876.80 seconds wall clock time: 105 minutes 14.11 seconds (6314.11 seconds total)