Starting phenix.real_space_refine on Fri Sep 27 20:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/09_2024/7xss_33433.cif" } resolution = 3.2 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= 0.003 sd= 0.037 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 54 5.49 5 S 55 5.16 5 C 10509 2.51 5 N 2928 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16847 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5361 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 3 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 438 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 10332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 10332 Classifications: {'peptide': 1282} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 60, 'TRANS': 1221} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" 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 10251 SG CYS B 491 51.531 61.380 43.574 1.00 60.61 S ATOM 10319 SG CYS B 501 52.869 59.111 41.007 1.00 78.43 S ATOM 10333 SG CYS B 503 50.624 62.101 39.975 1.00 63.44 S ATOM 10355 SG CYS B 506 54.129 62.759 41.028 1.00 61.94 S ATOM 12320 SG CYS B 750 37.086 68.987 69.699 1.00 82.00 S ATOM 12333 SG CYS B 752 35.703 72.353 68.473 1.00 76.41 S ATOM 12355 SG CYS B 755 39.381 71.473 67.865 1.00 66.60 S ATOM 14333 SG CYS B1018 40.584 94.375 98.167 1.00 72.20 S ATOM 14504 SG CYS B1406 40.785 90.807 97.058 1.00 61.86 S ATOM 14555 SG CYS B1414 37.418 92.784 96.977 1.00 67.22 S ATOM 14572 SG CYS B1417 40.053 93.446 94.418 1.00 58.03 S ATOM 7187 SG CYS B 88 73.014 51.784 19.001 1.00 75.41 S ATOM 7458 SG CYS B 121 75.863 50.427 16.716 1.00 90.38 S ATOM 7504 SG CYS B 127 75.564 54.021 17.405 1.00 77.54 S ATOM 7528 SG CYS B 130 76.582 51.697 20.272 1.00 72.67 S Time building chain proxies: 9.48, per 1000 atoms: 0.56 Number of scatterers: 16847 At special positions: 0 Unit cell: (107.67, 152.29, 132.89, 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 55 16.00 P 54 15.00 O 3297 8.00 N 2928 7.00 C 10509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 506 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 752 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1406 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 130 " Number of angles added : 21 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 39.4% alpha, 16.9% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.668A pdb=" N ASN C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 59 removed outlier: 4.053A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.625A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 110 removed outlier: 4.095A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.920A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.330A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.674A pdb=" N GLN C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.796A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.543A pdb=" N LYS C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 474 removed outlier: 3.684A pdb=" N PHE C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.551A pdb=" N GLY C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.694A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.744A pdb=" N LEU C 611 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.766A pdb=" N GLY C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 677 removed outlier: 3.570A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 677 " --> pdb=" O ILE C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 4.472A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 692 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.652A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.682A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.528A pdb=" N ALA B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.703A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.565A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 617 through 624 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.523A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 Processing helix chain 'B' and resid 752 through 758 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.618A pdb=" N GLU B 779 " --> pdb=" O ASN B 776 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 780' Processing helix chain 'B' and resid 831 through 848 removed outlier: 3.840A pdb=" N GLY B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 removed outlier: 3.613A pdb=" N GLY B 859 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 removed outlier: 3.790A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.724A pdb=" N ASP B 914 " --> pdb=" O SER B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.901A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.595A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B1399 " --> pdb=" O LEU B1395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1394 through 1399' Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.249A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.972A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B1493 " --> pdb=" O ILE B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1501 removed outlier: 4.147A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1501 " --> pdb=" O ILE B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1552 through 1556 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.558A pdb=" N GLY B1603 " --> pdb=" O ILE B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.662A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'C' and resid 425 through 431 Processing sheet with id=AA2, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.355A pdb=" N LEU C 580 " --> pdb=" O ILE C 623 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY C 625 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 582 " --> pdb=" O GLY C 625 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N CYS C 627 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 626 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 181 removed outlier: 4.230A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 11 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 238 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.268A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.690A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.579A pdb=" N SER B 517 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 533 removed outlier: 10.509A pdb=" N GLU B 526 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASP B 547 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ARG B 528 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 545 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ARG B 530 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N GLY B 543 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 532 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 865 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 787 through 792 removed outlier: 6.446A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 951 " --> pdb=" O THR B1569 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B1569 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 953 " --> pdb=" O LEU B1567 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B1567 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 955 " --> pdb=" O ASP B1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 967 through 968 removed outlier: 4.449A pdb=" N LYS B 988 " --> pdb=" O ASP B 968 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 989 " --> pdb=" O GLU B1510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1421 through 1422 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5262 1.34 - 1.46: 3315 1.46 - 1.58: 8572 1.58 - 1.70: 107 1.70 - 1.82: 76 Bond restraints: 17332 Sorted by residual: bond pdb=" CA ASN B 973 " pdb=" CB ASN B 973 " ideal model delta sigma weight residual 1.528 1.576 -0.048 1.67e-02 3.59e+03 8.20e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" N ASN B1544 " pdb=" CA ASN B1544 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C ARG B1644 " pdb=" N TYR B1645 " ideal model delta sigma weight residual 1.333 1.374 -0.041 2.74e-02 1.33e+03 2.26e+00 bond pdb=" CB ASP B1565 " pdb=" CG ASP B1565 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 17327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 23232 2.05 - 4.11: 340 4.11 - 6.16: 46 6.16 - 8.21: 6 8.21 - 10.27: 3 Bond angle restraints: 23627 Sorted by residual: angle pdb=" CA PRO B 86 " pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 112.00 102.06 9.94 1.40e+00 5.10e-01 5.04e+01 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 113.10 109.69 3.41 9.70e-01 1.06e+00 1.24e+01 angle pdb=" CA GLU B1496 " pdb=" CB GLU B1496 " pdb=" CG GLU B1496 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA GLU C 268 " pdb=" CB GLU C 268 " pdb=" CG GLU C 268 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ASP B1471 " pdb=" C ASP B1471 " pdb=" N GLU B1472 " ideal model delta sigma weight residual 116.84 122.20 -5.36 1.71e+00 3.42e-01 9.83e+00 ... (remaining 23622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9980 35.92 - 71.83: 463 71.83 - 107.74: 34 107.74 - 143.66: 0 143.66 - 179.57: 4 Dihedral angle restraints: 10481 sinusoidal: 4888 harmonic: 5593 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 43.53 156.47 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 51.57 -179.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D -14 " pdb=" C1' U D -14 " pdb=" N1 U D -14 " pdb=" C2 U D -14 " ideal model delta sinusoidal sigma weight residual -128.00 47.29 -175.29 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 10478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1936 0.040 - 0.079: 473 0.079 - 0.119: 136 0.119 - 0.158: 18 0.158 - 0.198: 3 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C1' A D -16 " pdb=" O4' A D -16 " pdb=" C2' A D -16 " pdb=" N9 A D -16 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASN B1544 " pdb=" N ASN B1544 " pdb=" C ASN B1544 " pdb=" CB ASN B1544 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 2563 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 85 " -0.097 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO B 86 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 439 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 440 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 37 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO C 38 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.035 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 452 2.69 - 3.25: 15678 3.25 - 3.80: 25665 3.80 - 4.35: 33989 4.35 - 4.90: 56432 Nonbonded interactions: 132216 Sorted by model distance: nonbonded pdb=" O ALA C 626 " pdb=" OG1 THR C 660 " model vdw 2.143 3.040 nonbonded pdb=" NZ LYS B1571 " pdb=" OD1 ASN B1573 " model vdw 2.145 3.120 nonbonded pdb=" OP2 U D 6 " pdb=" OG SER B 854 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR B1436 " pdb=" OE2 GLU B1441 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR B 191 " pdb=" OD2 ASP B 386 " model vdw 2.174 3.040 ... (remaining 132211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.003 0.135 17332 Z= 0.196 Angle : 0.613 10.265 23627 Z= 0.346 Chirality : 0.039 0.198 2566 Planarity : 0.005 0.138 2844 Dihedral : 19.020 179.575 6887 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer: Outliers : 0.59 % Allowed : 27.57 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.24 (0.19), residues: 1924 helix: 1.43 (0.21), residues: 630 sheet: 0.88 (0.32), residues: 270 loop : -1.57 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.009 0.001 HIS B1621 PHE 0.019 0.001 PHE B1570 TYR 0.021 0.001 TYR C 696 ARG 0.009 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 365 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 GLU cc_start: 0.6278 (tm-30) cc_final: 0.6020 (tm-30) REVERT: C 250 LEU cc_start: 0.8337 (tt) cc_final: 0.8129 (tp) REVERT: C 518 TYR cc_start: 0.7400 (t80) cc_final: 0.7196 (t80) REVERT: C 630 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.5300 (m-30) REVERT: B 744 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7599 (mtpt) REVERT: B 836 LEU cc_start: 0.8269 (mp) cc_final: 0.7978 (mt) REVERT: B 973 ASN cc_start: 0.8289 (p0) cc_final: 0.8016 (p0) outliers start: 10 outliers final: 4 residues processed: 370 average time/residue: 0.3547 time to fit residues: 185.0585 Evaluate side-chains 349 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 344 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 348 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 553 ASN C 612 ASN B 112 GLN B 335 GLN B 668 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 17332 Z= 0.534 Angle : 0.722 8.937 23627 Z= 0.378 Chirality : 0.049 0.272 2566 Planarity : 0.006 0.094 2844 Dihedral : 15.455 177.833 2945 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.16 % Allowed : 22.76 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.59 (0.19), residues: 1924 helix: 1.05 (0.20), residues: 638 sheet: 0.49 (0.33), residues: 260 loop : -1.64 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 612 HIS 0.008 0.002 HIS B 924 PHE 0.024 0.003 PHE B 156 TYR 0.025 0.003 TYR B 860 ARG 0.013 0.001 ARG B1491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 403 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 120 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7579 (mtp85) REVERT: C 134 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7473 (ttp80) REVERT: C 161 ASP cc_start: 0.7182 (m-30) cc_final: 0.6684 (t0) REVERT: C 216 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6477 (ptt) REVERT: C 218 LYS cc_start: 0.8005 (tptt) cc_final: 0.7758 (mtmm) REVERT: C 266 GLU cc_start: 0.7725 (tp30) cc_final: 0.7397 (tp30) REVERT: C 267 LYS cc_start: 0.8197 (mttp) cc_final: 0.7935 (mmmm) REVERT: C 508 LYS cc_start: 0.8382 (tppt) cc_final: 0.7817 (mmtm) REVERT: C 560 SER cc_start: 0.8224 (m) cc_final: 0.7881 (p) REVERT: C 585 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7809 (m90) REVERT: C 650 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (mp) REVERT: B 34 SER cc_start: 0.8612 (m) cc_final: 0.8281 (t) REVERT: B 142 VAL cc_start: 0.7805 (t) cc_final: 0.7519 (m) REVERT: B 171 ASP cc_start: 0.7705 (p0) cc_final: 0.7460 (t0) REVERT: B 313 LYS cc_start: 0.7899 (ptpp) cc_final: 0.7615 (mtmt) REVERT: B 349 SER cc_start: 0.8504 (p) cc_final: 0.8169 (m) REVERT: B 448 ASP cc_start: 0.6559 (t70) cc_final: 0.6278 (t70) REVERT: B 561 LEU cc_start: 0.8519 (tt) cc_final: 0.8239 (tp) REVERT: B 751 THR cc_start: 0.8790 (m) cc_final: 0.8547 (t) REVERT: B 849 LEU cc_start: 0.8627 (mt) cc_final: 0.8370 (mt) REVERT: B 933 VAL cc_start: 0.8494 (t) cc_final: 0.8240 (m) REVERT: B 973 ASN cc_start: 0.8270 (p0) cc_final: 0.7981 (p0) REVERT: B 1496 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 1557 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7994 (t80) REVERT: B 1570 PHE cc_start: 0.8398 (p90) cc_final: 0.8133 (p90) REVERT: B 1675 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7787 (ptmt) outliers start: 88 outliers final: 49 residues processed: 451 average time/residue: 0.3401 time to fit residues: 218.3169 Evaluate side-chains 430 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 376 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1675 LYS Chi-restraints excluded: chain B residue 1682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN C 576 ASN B 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17332 Z= 0.214 Angle : 0.566 6.280 23627 Z= 0.297 Chirality : 0.042 0.213 2566 Planarity : 0.005 0.075 2844 Dihedral : 15.303 178.555 2933 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.28 % Allowed : 22.99 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.19), residues: 1924 helix: 1.41 (0.20), residues: 633 sheet: 0.39 (0.33), residues: 259 loop : -1.51 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 612 HIS 0.015 0.001 HIS C 514 PHE 0.018 0.001 PHE C 491 TYR 0.016 0.001 TYR B 860 ARG 0.005 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 386 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7176 (tm-30) REVERT: C 161 ASP cc_start: 0.7133 (m-30) cc_final: 0.6627 (t0) REVERT: C 164 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6324 (tm-30) REVERT: C 214 GLU cc_start: 0.7370 (tt0) cc_final: 0.6954 (tt0) REVERT: C 216 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6293 (ptt) REVERT: C 218 LYS cc_start: 0.8017 (tptt) cc_final: 0.7762 (mtmm) REVERT: C 266 GLU cc_start: 0.7696 (tp30) cc_final: 0.6975 (tp30) REVERT: C 267 LYS cc_start: 0.8068 (mttp) cc_final: 0.7817 (mmmm) REVERT: C 273 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7867 (mtt90) REVERT: C 508 LYS cc_start: 0.8214 (tppt) cc_final: 0.7785 (mmtm) REVERT: C 560 SER cc_start: 0.8188 (m) cc_final: 0.7853 (p) REVERT: C 641 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6824 (tm-30) REVERT: C 663 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8521 (mttp) REVERT: C 685 ASN cc_start: 0.7373 (t0) cc_final: 0.7138 (t0) REVERT: B 34 SER cc_start: 0.8570 (m) cc_final: 0.8246 (t) REVERT: B 142 VAL cc_start: 0.7861 (t) cc_final: 0.7563 (m) REVERT: B 178 LEU cc_start: 0.8907 (mt) cc_final: 0.8622 (mp) REVERT: B 276 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7473 (mm110) REVERT: B 313 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7598 (mtmt) REVERT: B 349 SER cc_start: 0.8465 (p) cc_final: 0.8120 (m) REVERT: B 357 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7548 (mmmm) REVERT: B 361 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: B 448 ASP cc_start: 0.6690 (t70) cc_final: 0.6441 (t70) REVERT: B 454 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 561 LEU cc_start: 0.8481 (tt) cc_final: 0.8216 (tp) REVERT: B 591 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8385 (pp) REVERT: B 617 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7781 (mmtt) REVERT: B 644 ASP cc_start: 0.6854 (t0) cc_final: 0.6643 (m-30) REVERT: B 738 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7806 (mmt180) REVERT: B 928 ASP cc_start: 0.6831 (p0) cc_final: 0.6592 (p0) REVERT: B 933 VAL cc_start: 0.8469 (t) cc_final: 0.8192 (m) REVERT: B 973 ASN cc_start: 0.8278 (p0) cc_final: 0.7978 (p0) REVERT: B 997 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7837 (ttm) REVERT: B 1443 LEU cc_start: 0.7775 (tp) cc_final: 0.7524 (tp) REVERT: B 1496 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 1557 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7990 (t80) REVERT: B 1570 PHE cc_start: 0.8392 (p90) cc_final: 0.7542 (p90) REVERT: B 1691 PHE cc_start: 0.8081 (t80) cc_final: 0.7862 (t80) outliers start: 73 outliers final: 49 residues processed: 423 average time/residue: 0.3535 time to fit residues: 214.9282 Evaluate side-chains 432 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 377 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 51 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 553 ASN B 335 GLN B 498 GLN B1649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.198 Angle : 0.546 6.161 23627 Z= 0.286 Chirality : 0.041 0.215 2566 Planarity : 0.005 0.069 2844 Dihedral : 15.263 179.420 2933 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.46 % Allowed : 23.23 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.23 (0.19), residues: 1924 helix: 1.55 (0.20), residues: 634 sheet: 0.44 (0.34), residues: 243 loop : -1.46 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.013 0.001 TYR B 860 ARG 0.006 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 391 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 161 ASP cc_start: 0.7107 (m-30) cc_final: 0.6608 (t0) REVERT: C 164 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6189 (tm-30) REVERT: C 214 GLU cc_start: 0.7357 (tt0) cc_final: 0.7106 (tt0) REVERT: C 216 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6286 (ptt) REVERT: C 266 GLU cc_start: 0.7691 (tp30) cc_final: 0.6951 (tp30) REVERT: C 267 LYS cc_start: 0.8090 (mttp) cc_final: 0.7823 (mmmm) REVERT: C 273 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7790 (mtt90) REVERT: C 483 ASP cc_start: 0.7775 (t70) cc_final: 0.7304 (t70) REVERT: C 508 LYS cc_start: 0.8061 (tppt) cc_final: 0.7690 (mmtm) REVERT: C 641 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6811 (tm-30) REVERT: C 685 ASN cc_start: 0.7432 (t0) cc_final: 0.7219 (t0) REVERT: B 34 SER cc_start: 0.8557 (m) cc_final: 0.8353 (p) REVERT: B 142 VAL cc_start: 0.7823 (t) cc_final: 0.7537 (m) REVERT: B 178 LEU cc_start: 0.8907 (mt) cc_final: 0.8634 (mp) REVERT: B 313 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7591 (mtmt) REVERT: B 349 SER cc_start: 0.8450 (p) cc_final: 0.8109 (m) REVERT: B 448 ASP cc_start: 0.6759 (t70) cc_final: 0.6464 (t70) REVERT: B 454 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 591 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 617 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7677 (mmtt) REVERT: B 738 ARG cc_start: 0.8170 (tpp-160) cc_final: 0.7784 (mmt180) REVERT: B 751 THR cc_start: 0.8731 (m) cc_final: 0.8362 (t) REVERT: B 752 CYS cc_start: 0.7045 (p) cc_final: 0.6504 (p) REVERT: B 933 VAL cc_start: 0.8451 (t) cc_final: 0.8170 (m) REVERT: B 973 ASN cc_start: 0.8234 (p0) cc_final: 0.7935 (p0) REVERT: B 1496 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7112 (tm-30) REVERT: B 1557 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7972 (t80) REVERT: B 1691 PHE cc_start: 0.8078 (t80) cc_final: 0.7865 (t80) outliers start: 76 outliers final: 57 residues processed: 426 average time/residue: 0.3471 time to fit residues: 212.9545 Evaluate side-chains 438 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 376 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 553 ASN B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.219 Angle : 0.553 6.824 23627 Z= 0.289 Chirality : 0.041 0.223 2566 Planarity : 0.005 0.065 2844 Dihedral : 15.254 179.576 2933 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.16 % Allowed : 23.28 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.17 (0.19), residues: 1924 helix: 1.62 (0.20), residues: 634 sheet: 0.46 (0.33), residues: 243 loop : -1.43 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.020 0.001 PHE C 491 TYR 0.016 0.001 TYR B 578 ARG 0.006 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 388 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 161 ASP cc_start: 0.7057 (m-30) cc_final: 0.6564 (t0) REVERT: C 164 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6276 (tm-30) REVERT: C 187 LEU cc_start: 0.7777 (tp) cc_final: 0.7322 (tp) REVERT: C 214 GLU cc_start: 0.7269 (tt0) cc_final: 0.7059 (tt0) REVERT: C 218 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7593 (mtmm) REVERT: C 266 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: C 267 LYS cc_start: 0.8129 (mttp) cc_final: 0.7825 (mmmm) REVERT: C 273 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7767 (mtt90) REVERT: C 400 TRP cc_start: 0.8391 (m100) cc_final: 0.8020 (m100) REVERT: C 483 ASP cc_start: 0.7748 (t70) cc_final: 0.7003 (t70) REVERT: C 508 LYS cc_start: 0.8103 (tppt) cc_final: 0.7712 (mmtm) REVERT: C 641 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6791 (tm-30) REVERT: C 685 ASN cc_start: 0.7473 (t0) cc_final: 0.7245 (t0) REVERT: B 34 SER cc_start: 0.8549 (m) cc_final: 0.8335 (p) REVERT: B 142 VAL cc_start: 0.7820 (t) cc_final: 0.7547 (m) REVERT: B 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8606 (mp) REVERT: B 313 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7597 (mtmt) REVERT: B 349 SER cc_start: 0.8414 (p) cc_final: 0.8120 (m) REVERT: B 448 ASP cc_start: 0.6786 (t70) cc_final: 0.6471 (t70) REVERT: B 591 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 632 LYS cc_start: 0.7996 (mptt) cc_final: 0.7692 (mptt) REVERT: B 752 CYS cc_start: 0.7025 (p) cc_final: 0.6482 (p) REVERT: B 933 VAL cc_start: 0.8455 (t) cc_final: 0.8169 (m) REVERT: B 973 ASN cc_start: 0.8177 (p0) cc_final: 0.7871 (p0) REVERT: B 1496 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 1557 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 1593 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7882 (mtpp) REVERT: B 1691 PHE cc_start: 0.8085 (t80) cc_final: 0.7870 (t80) outliers start: 88 outliers final: 63 residues processed: 432 average time/residue: 0.3527 time to fit residues: 218.6739 Evaluate side-chains 440 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 373 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.0970 chunk 173 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 192 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN B1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17332 Z= 0.151 Angle : 0.528 9.397 23627 Z= 0.275 Chirality : 0.040 0.199 2566 Planarity : 0.004 0.062 2844 Dihedral : 15.195 179.608 2933 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.81 % Allowed : 24.69 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.05 (0.19), residues: 1924 helix: 1.79 (0.20), residues: 634 sheet: 0.36 (0.33), residues: 251 loop : -1.37 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.021 0.001 PHE C 491 TYR 0.015 0.001 TYR B 578 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 387 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 161 ASP cc_start: 0.7058 (m-30) cc_final: 0.6567 (t0) REVERT: C 187 LEU cc_start: 0.7726 (tp) cc_final: 0.7356 (tp) REVERT: C 266 GLU cc_start: 0.7660 (tp30) cc_final: 0.6925 (tp30) REVERT: C 267 LYS cc_start: 0.8046 (mttp) cc_final: 0.7787 (mmmm) REVERT: C 502 GLU cc_start: 0.7715 (pm20) cc_final: 0.7454 (pm20) REVERT: C 508 LYS cc_start: 0.8008 (tppt) cc_final: 0.7313 (mmtm) REVERT: C 599 LYS cc_start: 0.8021 (tppt) cc_final: 0.7644 (ttmm) REVERT: C 685 ASN cc_start: 0.7449 (t0) cc_final: 0.7217 (t0) REVERT: B 34 SER cc_start: 0.8552 (m) cc_final: 0.8329 (p) REVERT: B 178 LEU cc_start: 0.8862 (mt) cc_final: 0.8591 (mp) REVERT: B 185 THR cc_start: 0.8679 (p) cc_final: 0.8456 (t) REVERT: B 313 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7583 (mtmt) REVERT: B 349 SER cc_start: 0.8412 (p) cc_final: 0.8119 (m) REVERT: B 448 ASP cc_start: 0.6789 (t70) cc_final: 0.6542 (t70) REVERT: B 591 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8313 (pp) REVERT: B 597 THR cc_start: 0.8015 (p) cc_final: 0.7197 (t) REVERT: B 737 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8469 (mtm180) REVERT: B 751 THR cc_start: 0.8698 (m) cc_final: 0.8319 (t) REVERT: B 933 VAL cc_start: 0.8437 (t) cc_final: 0.8164 (m) REVERT: B 973 ASN cc_start: 0.8152 (p0) cc_final: 0.7858 (p0) REVERT: B 1496 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 1557 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7917 (t80) REVERT: B 1593 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7880 (mtpp) REVERT: B 1691 PHE cc_start: 0.8028 (t80) cc_final: 0.7802 (t80) outliers start: 65 outliers final: 44 residues processed: 418 average time/residue: 0.3369 time to fit residues: 203.3064 Evaluate side-chains 419 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 372 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 576 ASN B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.207 Angle : 0.552 8.354 23627 Z= 0.287 Chirality : 0.041 0.215 2566 Planarity : 0.004 0.061 2844 Dihedral : 15.209 179.604 2933 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.34 % Allowed : 24.52 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.04 (0.19), residues: 1924 helix: 1.79 (0.20), residues: 636 sheet: 0.38 (0.33), residues: 251 loop : -1.37 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.015 0.001 TYR B 578 ARG 0.004 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 380 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7037 (m-30) cc_final: 0.6543 (t0) REVERT: C 187 LEU cc_start: 0.7716 (tp) cc_final: 0.7353 (tp) REVERT: C 218 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7377 (mtmm) REVERT: C 266 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: C 267 LYS cc_start: 0.8130 (mttp) cc_final: 0.7829 (mmmm) REVERT: C 508 LYS cc_start: 0.8053 (tppt) cc_final: 0.7708 (mmtm) REVERT: C 585 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7546 (m90) REVERT: C 599 LYS cc_start: 0.8074 (tppt) cc_final: 0.7749 (ttmm) REVERT: C 685 ASN cc_start: 0.7500 (t0) cc_final: 0.7179 (t0) REVERT: B 34 SER cc_start: 0.8565 (m) cc_final: 0.8247 (t) REVERT: B 178 LEU cc_start: 0.8871 (mt) cc_final: 0.8612 (mp) REVERT: B 313 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7456 (mtmm) REVERT: B 349 SER cc_start: 0.8407 (p) cc_final: 0.8127 (m) REVERT: B 591 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (pp) REVERT: B 597 THR cc_start: 0.8058 (p) cc_final: 0.7249 (t) REVERT: B 717 GLU cc_start: 0.7101 (pm20) cc_final: 0.6844 (pm20) REVERT: B 752 CYS cc_start: 0.7012 (p) cc_final: 0.6471 (p) REVERT: B 933 VAL cc_start: 0.8439 (t) cc_final: 0.8173 (m) REVERT: B 973 ASN cc_start: 0.8134 (p0) cc_final: 0.7817 (p0) REVERT: B 1496 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 1557 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 1593 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7893 (mtpp) REVERT: B 1691 PHE cc_start: 0.8008 (t80) cc_final: 0.7470 (t80) outliers start: 74 outliers final: 58 residues processed: 413 average time/residue: 0.3369 time to fit residues: 200.7531 Evaluate side-chains 435 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 372 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN B1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.191 Angle : 0.549 8.329 23627 Z= 0.286 Chirality : 0.041 0.224 2566 Planarity : 0.004 0.063 2844 Dihedral : 15.209 179.600 2933 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.22 % Allowed : 24.63 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.00 (0.19), residues: 1924 helix: 1.84 (0.20), residues: 636 sheet: 0.37 (0.33), residues: 251 loop : -1.34 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.004 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 383 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7018 (m-30) cc_final: 0.6526 (t0) REVERT: C 187 LEU cc_start: 0.7701 (tp) cc_final: 0.7399 (tp) REVERT: C 218 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7355 (mtmm) REVERT: C 266 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: C 267 LYS cc_start: 0.8119 (mttp) cc_final: 0.7814 (mmmm) REVERT: C 502 GLU cc_start: 0.7674 (pm20) cc_final: 0.7424 (pm20) REVERT: C 508 LYS cc_start: 0.8071 (tppt) cc_final: 0.7298 (mmtm) REVERT: C 599 LYS cc_start: 0.7996 (tppt) cc_final: 0.7492 (ttmm) REVERT: C 685 ASN cc_start: 0.7541 (t0) cc_final: 0.7223 (t0) REVERT: B 178 LEU cc_start: 0.8873 (mt) cc_final: 0.8605 (mp) REVERT: B 218 LYS cc_start: 0.8530 (tppt) cc_final: 0.8271 (mmtm) REVERT: B 313 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7595 (mtmt) REVERT: B 349 SER cc_start: 0.8409 (p) cc_final: 0.8137 (m) REVERT: B 591 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8313 (pp) REVERT: B 597 THR cc_start: 0.8045 (p) cc_final: 0.7224 (t) REVERT: B 717 GLU cc_start: 0.7103 (pm20) cc_final: 0.6825 (pm20) REVERT: B 752 CYS cc_start: 0.6988 (p) cc_final: 0.6433 (p) REVERT: B 933 VAL cc_start: 0.8435 (t) cc_final: 0.8167 (m) REVERT: B 973 ASN cc_start: 0.8117 (p0) cc_final: 0.7818 (p0) REVERT: B 1496 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 1557 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7948 (t80) REVERT: B 1593 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7892 (mtpp) REVERT: B 1691 PHE cc_start: 0.8018 (t80) cc_final: 0.7180 (t80) outliers start: 72 outliers final: 58 residues processed: 412 average time/residue: 0.3381 time to fit residues: 200.1834 Evaluate side-chains 436 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 374 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 169 optimal weight: 0.0060 chunk 117 optimal weight: 0.0870 chunk 189 optimal weight: 0.6980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17332 Z= 0.169 Angle : 0.543 8.006 23627 Z= 0.282 Chirality : 0.040 0.241 2566 Planarity : 0.004 0.065 2844 Dihedral : 15.196 179.288 2933 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.58 % Allowed : 25.57 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.05 (0.19), residues: 1924 helix: 1.91 (0.20), residues: 636 sheet: 0.34 (0.33), residues: 251 loop : -1.32 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.013 0.001 TYR B 578 ARG 0.004 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 377 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7535 (ttp80) REVERT: C 161 ASP cc_start: 0.6997 (m-30) cc_final: 0.6534 (t0) REVERT: C 187 LEU cc_start: 0.7703 (tp) cc_final: 0.7412 (tp) REVERT: C 218 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7288 (mtmm) REVERT: C 266 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6900 (tp30) REVERT: C 267 LYS cc_start: 0.8101 (mttp) cc_final: 0.7834 (mmmm) REVERT: C 502 GLU cc_start: 0.7683 (pm20) cc_final: 0.7449 (pm20) REVERT: C 508 LYS cc_start: 0.8063 (tppt) cc_final: 0.7277 (mmtm) REVERT: C 599 LYS cc_start: 0.7773 (tppt) cc_final: 0.7335 (ttmm) REVERT: C 685 ASN cc_start: 0.7538 (t0) cc_final: 0.7218 (t0) REVERT: B 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8611 (mp) REVERT: B 218 LYS cc_start: 0.8518 (tppt) cc_final: 0.8267 (mmtm) REVERT: B 313 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7585 (mtmt) REVERT: B 349 SER cc_start: 0.8412 (p) cc_final: 0.8145 (m) REVERT: B 384 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7972 (mt) REVERT: B 591 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8303 (pp) REVERT: B 597 THR cc_start: 0.7988 (p) cc_final: 0.7162 (t) REVERT: B 633 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: B 737 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8458 (mtm180) REVERT: B 752 CYS cc_start: 0.6975 (p) cc_final: 0.6430 (p) REVERT: B 933 VAL cc_start: 0.8433 (t) cc_final: 0.8164 (m) REVERT: B 973 ASN cc_start: 0.8109 (p0) cc_final: 0.7811 (p0) REVERT: B 1496 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7074 (tm-30) REVERT: B 1512 MET cc_start: 0.7355 (mtp) cc_final: 0.7099 (mmm) REVERT: B 1557 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7916 (t80) REVERT: B 1593 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7891 (mtpp) REVERT: B 1689 ASN cc_start: 0.7223 (t0) cc_final: 0.6947 (t0) outliers start: 61 outliers final: 50 residues processed: 400 average time/residue: 0.3349 time to fit residues: 192.2740 Evaluate side-chains 431 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 375 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 198 optimal weight: 0.2980 chunk 182 optimal weight: 0.9990 chunk 157 optimal weight: 0.0040 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 415 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.175 Angle : 0.544 7.408 23627 Z= 0.283 Chirality : 0.040 0.242 2566 Planarity : 0.004 0.067 2844 Dihedral : 15.193 179.142 2933 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.70 % Allowed : 25.45 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.07 (0.19), residues: 1924 helix: 1.93 (0.20), residues: 636 sheet: 0.36 (0.33), residues: 252 loop : -1.32 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.020 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.006 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 378 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7543 (ttp80) REVERT: C 161 ASP cc_start: 0.6989 (m-30) cc_final: 0.6524 (t0) REVERT: C 187 LEU cc_start: 0.7698 (tp) cc_final: 0.7454 (tp) REVERT: C 218 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7273 (mtmm) REVERT: C 266 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: C 267 LYS cc_start: 0.8104 (mttp) cc_final: 0.7836 (mmmm) REVERT: C 282 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6902 (ttm170) REVERT: C 502 GLU cc_start: 0.7677 (pm20) cc_final: 0.7459 (pm20) REVERT: C 508 LYS cc_start: 0.8086 (tppt) cc_final: 0.7322 (mmtm) REVERT: C 599 LYS cc_start: 0.7753 (tppt) cc_final: 0.7312 (ttmm) REVERT: C 685 ASN cc_start: 0.7565 (t0) cc_final: 0.7250 (t0) REVERT: B 178 LEU cc_start: 0.8878 (mt) cc_final: 0.8609 (mp) REVERT: B 185 THR cc_start: 0.8663 (p) cc_final: 0.8461 (t) REVERT: B 218 LYS cc_start: 0.8517 (tppt) cc_final: 0.8263 (mmtm) REVERT: B 313 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7571 (mtmt) REVERT: B 349 SER cc_start: 0.8415 (p) cc_final: 0.8144 (m) REVERT: B 384 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 591 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8291 (pp) REVERT: B 597 THR cc_start: 0.8000 (p) cc_final: 0.7200 (t) REVERT: B 933 VAL cc_start: 0.8434 (t) cc_final: 0.8163 (m) REVERT: B 973 ASN cc_start: 0.8099 (p0) cc_final: 0.7799 (p0) REVERT: B 1496 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 1512 MET cc_start: 0.7361 (mtp) cc_final: 0.7106 (mmm) REVERT: B 1557 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 1593 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7883 (mtpp) REVERT: B 1689 ASN cc_start: 0.7201 (t0) cc_final: 0.6874 (t0) outliers start: 63 outliers final: 50 residues processed: 403 average time/residue: 0.3481 time to fit residues: 201.2051 Evaluate side-chains 429 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 374 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 480 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109628 restraints weight = 24274.681| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3237 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17332 Z= 0.186 Angle : 0.555 10.282 23627 Z= 0.288 Chirality : 0.041 0.237 2566 Planarity : 0.004 0.067 2844 Dihedral : 15.198 179.182 2933 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.70 % Allowed : 25.51 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.07 (0.19), residues: 1924 helix: 1.94 (0.20), residues: 636 sheet: 0.39 (0.33), residues: 252 loop : -1.33 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.018 0.001 TYR B 202 ARG 0.006 0.000 ARG C 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.25 seconds wall clock time: 83 minutes 50.69 seconds (5030.69 seconds total)