Starting phenix.real_space_refine on Sun Jun 15 08:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_33433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_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/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_33433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_33433.map" model { file = "/net/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_33433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xss_33433/06_2025/7xss_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.57, per 1000 atoms: 0.63 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: 4.10 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: 6.03 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: 7.03 Time building geometry restraints manager: 4.92 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: 1.440 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 48.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- 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 17348 Z= 0.127 Angle : 0.619 10.265 23648 Z= 0.347 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 Details of bonding type rmsd hydrogen bonds : bond 0.17429 ( 606) hydrogen bonds : angle 5.78758 ( 1780) metal coordination : bond 0.00428 ( 16) metal coordination : angle 2.96188 ( 21) covalent geometry : bond 0.00271 (17332) covalent geometry : angle 0.61267 (23627) *********************** 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 to be fit. rotamer outliers: 10 poor density : 365 time to evaluate : 1.840 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: 0.3562 time to fit residues: 185.7669 Evaluate side-chains 349 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 344 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105500 restraints weight = 24745.545| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.99 r_work: 0.3156 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 17348 Z= 0.351 Angle : 0.731 8.937 23648 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 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 606) hydrogen bonds : angle 4.40755 ( 1780) metal coordination : bond 0.01489 ( 16) metal coordination : angle 3.84558 ( 21) covalent geometry : bond 0.00824 (17332) covalent geometry : angle 0.72217 (23627) *********************** 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 to be fit. rotamer outliers: 88 poor density : 403 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6931 (mp0) REVERT: C 102 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7318 (tm-30) REVERT: C 120 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7639 (mtp85) REVERT: C 134 ARG cc_start: 0.8188 (tmm-80) cc_final: 0.7740 (ttp80) REVERT: C 161 ASP cc_start: 0.7312 (m-30) cc_final: 0.6680 (t0) REVERT: C 164 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6463 (tm-30) REVERT: C 214 GLU cc_start: 0.7770 (tt0) cc_final: 0.7566 (tt0) REVERT: C 216 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6493 (ptt) REVERT: C 218 LYS cc_start: 0.7981 (tptt) cc_final: 0.7610 (mtmm) REVERT: C 266 GLU cc_start: 0.7848 (tp30) cc_final: 0.7506 (tp30) REVERT: C 267 LYS cc_start: 0.8365 (mttp) cc_final: 0.8085 (mmmm) REVERT: C 508 LYS cc_start: 0.8375 (tppt) cc_final: 0.7804 (mmtm) REVERT: C 560 SER cc_start: 0.8288 (m) cc_final: 0.7891 (p) REVERT: C 585 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7817 (m90) REVERT: C 650 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 34 SER cc_start: 0.8530 (m) cc_final: 0.8181 (t) REVERT: B 95 ASP cc_start: 0.7580 (t0) cc_final: 0.7369 (t0) REVERT: B 142 VAL cc_start: 0.7833 (t) cc_final: 0.7465 (m) REVERT: B 171 ASP cc_start: 0.7738 (p0) cc_final: 0.7420 (t0) REVERT: B 313 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7615 (mtmt) REVERT: B 349 SER cc_start: 0.8442 (p) cc_final: 0.8156 (m) REVERT: B 409 GLU cc_start: 0.7633 (mp0) cc_final: 0.7415 (pm20) REVERT: B 448 ASP cc_start: 0.6448 (t70) cc_final: 0.6168 (t70) REVERT: B 561 LEU cc_start: 0.8381 (tt) cc_final: 0.8101 (tp) REVERT: B 719 ARG cc_start: 0.7622 (ptp-170) cc_final: 0.7390 (ptp-170) REVERT: B 751 THR cc_start: 0.8817 (m) cc_final: 0.8578 (t) REVERT: B 849 LEU cc_start: 0.8638 (mt) cc_final: 0.8366 (mt) REVERT: B 933 VAL cc_start: 0.8481 (t) cc_final: 0.8212 (m) REVERT: B 973 ASN cc_start: 0.8298 (p0) cc_final: 0.8015 (p0) REVERT: B 1496 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 1557 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 1570 PHE cc_start: 0.8358 (p90) cc_final: 0.8070 (p90) REVERT: B 1675 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7967 (ptmt) outliers start: 88 outliers final: 49 residues processed: 451 average time/residue: 0.3510 time to fit residues: 225.4253 Evaluate side-chains 429 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108255 restraints weight = 24218.261| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.96 r_work: 0.3198 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17348 Z= 0.156 Angle : 0.584 9.084 23648 Z= 0.302 Chirality : 0.042 0.222 2566 Planarity : 0.005 0.076 2844 Dihedral : 15.319 178.241 2933 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.63 % Allowed : 22.82 % Favored : 72.55 % 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: -0.40 (0.19), residues: 1924 helix: 1.34 (0.20), residues: 639 sheet: 0.37 (0.32), residues: 260 loop : -1.55 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 PHE 0.019 0.001 PHE C 491 TYR 0.016 0.001 TYR B 860 ARG 0.004 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 606) hydrogen bonds : angle 4.09464 ( 1780) metal coordination : bond 0.00786 ( 16) metal coordination : angle 3.42162 ( 21) covalent geometry : bond 0.00359 (17332) covalent geometry : angle 0.57554 (23627) *********************** 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 468 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 389 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 120 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7634 (mtp85) REVERT: C 161 ASP cc_start: 0.7260 (m-30) cc_final: 0.6628 (t0) REVERT: C 214 GLU cc_start: 0.7730 (tt0) cc_final: 0.7343 (tt0) REVERT: C 216 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6393 (ptt) REVERT: C 218 LYS cc_start: 0.8009 (tptt) cc_final: 0.7614 (mtmm) REVERT: C 249 THR cc_start: 0.8442 (p) cc_final: 0.8205 (t) REVERT: C 266 GLU cc_start: 0.7817 (tp30) cc_final: 0.7135 (tp30) REVERT: C 267 LYS cc_start: 0.8281 (mttp) cc_final: 0.7996 (mmmm) REVERT: C 273 ARG cc_start: 0.8384 (mtt90) cc_final: 0.8072 (mtt90) REVERT: C 508 LYS cc_start: 0.8236 (tppt) cc_final: 0.7798 (mmtm) REVERT: C 547 PHE cc_start: 0.7011 (m-80) cc_final: 0.6799 (m-80) REVERT: C 560 SER cc_start: 0.8241 (m) cc_final: 0.7842 (p) REVERT: C 641 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6794 (tm-30) REVERT: C 663 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8491 (mttp) REVERT: C 685 ASN cc_start: 0.7367 (t0) cc_final: 0.7141 (t0) REVERT: C 697 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8171 (ttpt) REVERT: B 34 SER cc_start: 0.8521 (m) cc_final: 0.8160 (t) REVERT: B 95 ASP cc_start: 0.7522 (t0) cc_final: 0.7297 (t0) REVERT: B 142 VAL cc_start: 0.7832 (t) cc_final: 0.7451 (m) REVERT: B 171 ASP cc_start: 0.7657 (p0) cc_final: 0.7454 (t0) REVERT: B 178 LEU cc_start: 0.8871 (mt) cc_final: 0.8571 (mp) REVERT: B 313 LYS cc_start: 0.7907 (ptpp) cc_final: 0.7580 (mtmt) REVERT: B 349 SER cc_start: 0.8366 (p) cc_final: 0.8098 (m) REVERT: B 357 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7677 (mtpp) REVERT: B 361 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7331 (mpp) REVERT: B 448 ASP cc_start: 0.6590 (t70) cc_final: 0.6301 (t70) REVERT: B 454 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 561 LEU cc_start: 0.8309 (tt) cc_final: 0.8055 (tp) REVERT: B 591 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8313 (pp) REVERT: B 617 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7764 (mmtt) REVERT: B 644 ASP cc_start: 0.7103 (t0) cc_final: 0.6852 (m-30) REVERT: B 738 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8054 (mmt180) REVERT: B 744 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7643 (mtmt) REVERT: B 933 VAL cc_start: 0.8496 (t) cc_final: 0.8219 (m) REVERT: B 973 ASN cc_start: 0.8291 (p0) cc_final: 0.7989 (p0) REVERT: B 997 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: B 1443 LEU cc_start: 0.7658 (tp) cc_final: 0.7435 (tp) REVERT: B 1496 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 1557 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7783 (t80) REVERT: B 1570 PHE cc_start: 0.8422 (p90) cc_final: 0.7493 (p90) REVERT: B 1675 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7846 (ptmt) REVERT: B 1691 PHE cc_start: 0.8088 (t80) cc_final: 0.7794 (t80) outliers start: 79 outliers final: 54 residues processed: 428 average time/residue: 0.3471 time to fit residues: 214.5167 Evaluate side-chains 438 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 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 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 8 ILE 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 239 VAL 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 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 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 Chi-restraints excluded: chain B residue 1675 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 36 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 514 HIS C 553 ASN B 335 GLN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107481 restraints weight = 24309.704| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.09 r_work: 0.3207 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 17348 Z= 0.138 Angle : 0.560 8.480 23648 Z= 0.289 Chirality : 0.042 0.219 2566 Planarity : 0.005 0.069 2844 Dihedral : 15.275 179.225 2933 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.81 % Allowed : 22.82 % Favored : 72.38 % 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: -0.26 (0.19), residues: 1924 helix: 1.52 (0.20), residues: 634 sheet: 0.45 (0.33), residues: 243 loop : -1.47 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.014 0.001 TYR B 860 ARG 0.005 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 606) hydrogen bonds : angle 3.94742 ( 1780) metal coordination : bond 0.00590 ( 16) metal coordination : angle 3.19644 ( 21) covalent geometry : bond 0.00317 (17332) covalent geometry : angle 0.55158 (23627) *********************** 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 470 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 388 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 161 ASP cc_start: 0.7250 (m-30) cc_final: 0.6635 (t0) REVERT: C 164 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6474 (tm-30) REVERT: C 214 GLU cc_start: 0.7700 (tt0) cc_final: 0.7273 (tt0) REVERT: C 216 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6371 (ptt) REVERT: C 218 LYS cc_start: 0.7986 (tptt) cc_final: 0.7618 (mtmm) REVERT: C 249 THR cc_start: 0.8532 (p) cc_final: 0.8302 (t) REVERT: C 266 GLU cc_start: 0.7854 (tp30) cc_final: 0.7159 (tp30) REVERT: C 267 LYS cc_start: 0.8310 (mttp) cc_final: 0.7999 (mmmm) REVERT: C 273 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8035 (mtt90) REVERT: C 483 ASP cc_start: 0.7917 (t70) cc_final: 0.7259 (t0) REVERT: C 508 LYS cc_start: 0.8147 (tppt) cc_final: 0.7762 (mmtm) REVERT: C 641 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6846 (tm-30) REVERT: C 663 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8559 (mttp) REVERT: B 34 SER cc_start: 0.8485 (m) cc_final: 0.8143 (t) REVERT: B 95 ASP cc_start: 0.7578 (t0) cc_final: 0.7367 (t0) REVERT: B 142 VAL cc_start: 0.7876 (t) cc_final: 0.7519 (m) REVERT: B 171 ASP cc_start: 0.7667 (p0) cc_final: 0.7389 (p0) REVERT: B 178 LEU cc_start: 0.8864 (mt) cc_final: 0.8582 (mp) REVERT: B 313 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7601 (mtmt) REVERT: B 349 SER cc_start: 0.8375 (p) cc_final: 0.8125 (m) REVERT: B 448 ASP cc_start: 0.6685 (t70) cc_final: 0.6354 (t70) REVERT: B 454 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 561 LEU cc_start: 0.8373 (tt) cc_final: 0.8127 (tp) REVERT: B 591 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 617 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7764 (mmtt) REVERT: B 644 ASP cc_start: 0.7220 (t0) cc_final: 0.6925 (m-30) REVERT: B 752 CYS cc_start: 0.7184 (p) cc_final: 0.6629 (p) REVERT: B 933 VAL cc_start: 0.8524 (t) cc_final: 0.8240 (m) REVERT: B 973 ASN cc_start: 0.8264 (p0) cc_final: 0.7946 (p0) REVERT: B 997 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: B 1496 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 1557 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 1691 PHE cc_start: 0.8068 (t80) cc_final: 0.7788 (t80) outliers start: 82 outliers final: 60 residues processed: 425 average time/residue: 0.3493 time to fit residues: 212.1041 Evaluate side-chains 450 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 384 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 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 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 295 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 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 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 719 ARG 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 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 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 129 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106392 restraints weight = 24532.525| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.09 r_work: 0.3173 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17348 Z= 0.187 Angle : 0.586 9.227 23648 Z= 0.303 Chirality : 0.043 0.250 2566 Planarity : 0.005 0.066 2844 Dihedral : 15.292 179.089 2933 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.75 % Allowed : 22.76 % 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: -0.28 (0.19), residues: 1924 helix: 1.50 (0.20), residues: 636 sheet: 0.38 (0.33), residues: 249 loop : -1.49 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 PHE 0.020 0.002 PHE C 491 TYR 0.014 0.001 TYR B 860 ARG 0.006 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 606) hydrogen bonds : angle 3.93126 ( 1780) metal coordination : bond 0.00778 ( 16) metal coordination : angle 3.32925 ( 21) covalent geometry : bond 0.00436 (17332) covalent geometry : angle 0.57825 (23627) *********************** 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 494 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 396 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 134 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7775 (ttp80) REVERT: C 161 ASP cc_start: 0.7196 (m-30) cc_final: 0.6593 (t0) REVERT: C 164 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6468 (tm-30) REVERT: C 187 LEU cc_start: 0.7678 (tp) cc_final: 0.7203 (tp) REVERT: C 214 GLU cc_start: 0.7751 (tt0) cc_final: 0.7343 (tt0) REVERT: C 216 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6383 (ptt) REVERT: C 218 LYS cc_start: 0.8001 (tptt) cc_final: 0.7716 (mtmm) REVERT: C 249 THR cc_start: 0.8560 (p) cc_final: 0.8331 (t) REVERT: C 257 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8174 (mtpt) REVERT: C 266 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: C 267 LYS cc_start: 0.8406 (mttp) cc_final: 0.8086 (mmmm) REVERT: C 483 ASP cc_start: 0.7923 (t70) cc_final: 0.7229 (t0) REVERT: C 508 LYS cc_start: 0.8191 (tppt) cc_final: 0.7789 (mmtm) REVERT: C 585 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7692 (m90) REVERT: C 641 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6865 (tm-30) REVERT: C 650 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8513 (mp) REVERT: C 663 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8619 (mttp) REVERT: B 95 ASP cc_start: 0.7570 (t0) cc_final: 0.7331 (t0) REVERT: B 142 VAL cc_start: 0.7918 (t) cc_final: 0.7561 (m) REVERT: B 171 ASP cc_start: 0.7644 (p0) cc_final: 0.7331 (p0) REVERT: B 178 LEU cc_start: 0.8841 (mt) cc_final: 0.8588 (mp) REVERT: B 313 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7626 (mtmt) REVERT: B 349 SER cc_start: 0.8389 (p) cc_final: 0.8158 (m) REVERT: B 448 ASP cc_start: 0.6782 (t70) cc_final: 0.6431 (t70) REVERT: B 454 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 561 LEU cc_start: 0.8364 (tt) cc_final: 0.8135 (tp) REVERT: B 617 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7730 (mmtt) REVERT: B 632 LYS cc_start: 0.8018 (mptt) cc_final: 0.7669 (mptt) REVERT: B 644 ASP cc_start: 0.7151 (t0) cc_final: 0.6877 (m-30) REVERT: B 744 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7674 (mtmt) REVERT: B 752 CYS cc_start: 0.7117 (p) cc_final: 0.6410 (p) REVERT: B 933 VAL cc_start: 0.8528 (t) cc_final: 0.8236 (m) REVERT: B 973 ASN cc_start: 0.8208 (p0) cc_final: 0.7870 (p0) REVERT: B 1496 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 1557 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7867 (t80) REVERT: B 1593 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8111 (mtpp) REVERT: B 1691 PHE cc_start: 0.8044 (t80) cc_final: 0.7473 (t80) outliers start: 98 outliers final: 69 residues processed: 448 average time/residue: 0.3426 time to fit residues: 219.2635 Evaluate side-chains 461 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 385 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 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 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 396 VAL 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 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 185 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 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 377 VAL 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 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 719 ARG 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 968 ASP 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 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 189 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107406 restraints weight = 24344.288| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.98 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17348 Z= 0.139 Angle : 0.569 8.788 23648 Z= 0.293 Chirality : 0.042 0.226 2566 Planarity : 0.005 0.063 2844 Dihedral : 15.278 179.535 2933 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.10 % Allowed : 23.23 % Favored : 71.67 % 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: -0.16 (0.19), residues: 1924 helix: 1.63 (0.20), residues: 636 sheet: 0.38 (0.33), residues: 249 loop : -1.42 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.021 0.001 PHE C 491 TYR 0.016 0.001 TYR B 578 ARG 0.007 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 606) hydrogen bonds : angle 3.84349 ( 1780) metal coordination : bond 0.00561 ( 16) metal coordination : angle 3.25232 ( 21) covalent geometry : bond 0.00322 (17332) covalent geometry : angle 0.56106 (23627) *********************** 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 479 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 392 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7498 (t0) cc_final: 0.6815 (m-30) REVERT: C 102 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7552 (tm-30) REVERT: C 161 ASP cc_start: 0.7127 (m-30) cc_final: 0.6509 (t0) REVERT: C 164 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6402 (tm-30) REVERT: C 187 LEU cc_start: 0.7617 (tp) cc_final: 0.7215 (tp) REVERT: C 214 GLU cc_start: 0.7687 (tt0) cc_final: 0.7268 (tt0) REVERT: C 216 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6311 (ptt) REVERT: C 218 LYS cc_start: 0.8009 (tptt) cc_final: 0.7742 (mtmm) REVERT: C 249 THR cc_start: 0.8542 (p) cc_final: 0.8323 (t) REVERT: C 266 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: C 267 LYS cc_start: 0.8359 (mttp) cc_final: 0.8042 (mmmm) REVERT: C 508 LYS cc_start: 0.8106 (tppt) cc_final: 0.7682 (mmtm) REVERT: C 585 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7603 (m90) REVERT: C 599 LYS cc_start: 0.8181 (tppt) cc_final: 0.7773 (ttmm) REVERT: C 663 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8630 (mttp) REVERT: B 36 MET cc_start: 0.8631 (tpt) cc_final: 0.8429 (mmm) REVERT: B 95 ASP cc_start: 0.7550 (t0) cc_final: 0.7291 (t0) REVERT: B 142 VAL cc_start: 0.7883 (t) cc_final: 0.7544 (m) REVERT: B 171 ASP cc_start: 0.7604 (p0) cc_final: 0.7283 (p0) REVERT: B 178 LEU cc_start: 0.8841 (mt) cc_final: 0.8576 (mp) REVERT: B 313 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7612 (mtmt) REVERT: B 349 SER cc_start: 0.8370 (p) cc_final: 0.8155 (m) REVERT: B 448 ASP cc_start: 0.6789 (t70) cc_final: 0.6444 (t70) REVERT: B 454 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 597 THR cc_start: 0.7987 (p) cc_final: 0.7203 (t) REVERT: B 617 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7658 (mmtt) REVERT: B 644 ASP cc_start: 0.7053 (t0) cc_final: 0.6816 (m-30) REVERT: B 717 GLU cc_start: 0.7295 (pm20) cc_final: 0.7025 (pm20) REVERT: B 744 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7608 (mtmt) REVERT: B 752 CYS cc_start: 0.7043 (p) cc_final: 0.6313 (p) REVERT: B 933 VAL cc_start: 0.8498 (t) cc_final: 0.8222 (m) REVERT: B 973 ASN cc_start: 0.8168 (p0) cc_final: 0.7835 (p0) REVERT: B 1496 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 1557 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 1593 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8073 (mtpp) outliers start: 87 outliers final: 68 residues processed: 435 average time/residue: 0.3402 time to fit residues: 212.5247 Evaluate side-chains 459 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 385 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 112 ASN Chi-restraints excluded: chain C residue 178 VAL 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 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 435 GLU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 515 SER 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 615 LYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 6 MET 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 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 451 VAL 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 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 719 ARG 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107021 restraints weight = 24356.843| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.98 r_work: 0.3205 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17348 Z= 0.157 Angle : 0.577 8.779 23648 Z= 0.298 Chirality : 0.042 0.234 2566 Planarity : 0.005 0.062 2844 Dihedral : 15.282 179.521 2933 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.04 % Allowed : 23.75 % Favored : 71.20 % 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: -0.14 (0.19), residues: 1924 helix: 1.64 (0.20), residues: 636 sheet: 0.37 (0.33), residues: 249 loop : -1.40 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 PHE 0.021 0.001 PHE C 491 TYR 0.015 0.001 TYR B 578 ARG 0.006 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 606) hydrogen bonds : angle 3.84276 ( 1780) metal coordination : bond 0.00659 ( 16) metal coordination : angle 3.19996 ( 21) covalent geometry : bond 0.00366 (17332) covalent geometry : angle 0.56938 (23627) *********************** 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 480 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 394 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7477 (t0) cc_final: 0.6823 (m-30) REVERT: C 102 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 161 ASP cc_start: 0.7125 (m-30) cc_final: 0.6533 (t0) REVERT: C 164 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6459 (tm-30) REVERT: C 187 LEU cc_start: 0.7652 (tp) cc_final: 0.7262 (tp) REVERT: C 214 GLU cc_start: 0.7665 (tt0) cc_final: 0.7211 (tt0) REVERT: C 216 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6330 (ptt) REVERT: C 218 LYS cc_start: 0.8024 (tptt) cc_final: 0.7734 (mtmm) REVERT: C 249 THR cc_start: 0.8533 (p) cc_final: 0.8308 (t) REVERT: C 257 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8110 (mtpt) REVERT: C 267 LYS cc_start: 0.8383 (mttp) cc_final: 0.8030 (mmmm) REVERT: C 354 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8470 (m) REVERT: C 508 LYS cc_start: 0.8174 (tppt) cc_final: 0.7776 (mmtm) REVERT: C 585 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7684 (m90) REVERT: C 599 LYS cc_start: 0.8158 (tppt) cc_final: 0.7745 (ttmm) REVERT: C 663 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8623 (mttm) REVERT: B 95 ASP cc_start: 0.7582 (t0) cc_final: 0.7330 (t0) REVERT: B 142 VAL cc_start: 0.7913 (t) cc_final: 0.7568 (m) REVERT: B 171 ASP cc_start: 0.7605 (p0) cc_final: 0.7293 (p0) REVERT: B 178 LEU cc_start: 0.8803 (mt) cc_final: 0.8554 (mp) REVERT: B 313 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7587 (mtmt) REVERT: B 448 ASP cc_start: 0.6866 (t70) cc_final: 0.6448 (t0) REVERT: B 449 SER cc_start: 0.7982 (m) cc_final: 0.7765 (p) REVERT: B 454 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 617 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7710 (mmtt) REVERT: B 644 ASP cc_start: 0.7092 (t0) cc_final: 0.6880 (m-30) REVERT: B 717 GLU cc_start: 0.7287 (pm20) cc_final: 0.7020 (pm20) REVERT: B 752 CYS cc_start: 0.7066 (p) cc_final: 0.6499 (p) REVERT: B 933 VAL cc_start: 0.8486 (t) cc_final: 0.8219 (m) REVERT: B 973 ASN cc_start: 0.8143 (p0) cc_final: 0.7791 (p0) REVERT: B 1496 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 1557 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 1593 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8053 (mtpp) outliers start: 86 outliers final: 70 residues processed: 433 average time/residue: 0.3516 time to fit residues: 218.7598 Evaluate side-chains 455 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 379 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU 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 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 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL 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 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 34 SER 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 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 451 VAL 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 617 LYS 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 719 ARG 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 879 MET Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 969 THR 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 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 157 optimal weight: 0.0570 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 357 GLN C 415 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 = 0.3555 r_free = 0.3555 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108223 restraints weight = 24226.672| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.96 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17348 Z= 0.129 Angle : 0.563 8.160 23648 Z= 0.290 Chirality : 0.041 0.219 2566 Planarity : 0.005 0.064 2844 Dihedral : 15.255 179.970 2933 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.75 % Allowed : 23.87 % Favored : 71.38 % 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: -0.09 (0.19), residues: 1924 helix: 1.75 (0.20), residues: 635 sheet: 0.32 (0.33), residues: 251 loop : -1.39 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.021 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.006 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 606) hydrogen bonds : angle 3.78752 ( 1780) metal coordination : bond 0.00506 ( 16) metal coordination : angle 3.08011 ( 21) covalent geometry : bond 0.00297 (17332) covalent geometry : angle 0.55601 (23627) *********************** 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 466 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7492 (t0) cc_final: 0.6837 (m-30) REVERT: C 102 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 161 ASP cc_start: 0.7090 (m-30) cc_final: 0.6492 (t0) REVERT: C 164 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6465 (tm-30) REVERT: C 187 LEU cc_start: 0.7576 (tp) cc_final: 0.7244 (tp) REVERT: C 216 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6295 (ptt) REVERT: C 218 LYS cc_start: 0.8006 (tptt) cc_final: 0.7741 (mtmm) REVERT: C 249 THR cc_start: 0.8505 (p) cc_final: 0.8272 (t) REVERT: C 250 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8384 (tt) REVERT: C 267 LYS cc_start: 0.8209 (mttp) cc_final: 0.7958 (mmmm) REVERT: C 273 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7896 (mtp85) REVERT: C 354 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8448 (m) REVERT: C 508 LYS cc_start: 0.8183 (tppt) cc_final: 0.7629 (mmtm) REVERT: C 585 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7642 (m90) REVERT: C 599 LYS cc_start: 0.8110 (tppt) cc_final: 0.7686 (ttmm) REVERT: C 688 GLN cc_start: 0.8076 (mt0) cc_final: 0.7663 (mt0) REVERT: B 95 ASP cc_start: 0.7558 (t0) cc_final: 0.7280 (t0) REVERT: B 142 VAL cc_start: 0.7879 (t) cc_final: 0.7526 (m) REVERT: B 171 ASP cc_start: 0.7599 (p0) cc_final: 0.7280 (p0) REVERT: B 178 LEU cc_start: 0.8819 (mt) cc_final: 0.8558 (mp) REVERT: B 238 GLU cc_start: 0.7921 (pm20) cc_final: 0.7701 (pm20) REVERT: B 313 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7530 (mtmt) REVERT: B 448 ASP cc_start: 0.6903 (t70) cc_final: 0.6509 (t0) REVERT: B 449 SER cc_start: 0.8028 (m) cc_final: 0.7801 (p) REVERT: B 454 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 617 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7669 (mmtt) REVERT: B 644 ASP cc_start: 0.7073 (t0) cc_final: 0.6843 (m-30) REVERT: B 744 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7689 (mtmt) REVERT: B 752 CYS cc_start: 0.6974 (p) cc_final: 0.6255 (p) REVERT: B 933 VAL cc_start: 0.8485 (t) cc_final: 0.8215 (m) REVERT: B 973 ASN cc_start: 0.8126 (p0) cc_final: 0.7795 (p0) REVERT: B 1496 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 1557 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 1593 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8053 (mtpp) outliers start: 81 outliers final: 65 residues processed: 423 average time/residue: 0.3449 time to fit residues: 209.7632 Evaluate side-chains 451 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 379 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 136 ASP Chi-restraints excluded: chain C residue 178 VAL 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 354 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL 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 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU 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 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 451 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS 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 719 ARG 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 854 SER Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 968 ASP 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 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 59 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 190 optimal weight: 0.0570 chunk 192 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108642 restraints weight = 24349.279| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.98 r_work: 0.3226 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17348 Z= 0.120 Angle : 0.556 7.903 23648 Z= 0.287 Chirality : 0.041 0.220 2566 Planarity : 0.005 0.066 2844 Dihedral : 15.233 179.656 2933 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.57 % Allowed : 24.16 % Favored : 71.26 % 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: -0.03 (0.19), residues: 1924 helix: 1.81 (0.20), residues: 635 sheet: 0.32 (0.33), residues: 251 loop : -1.36 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.022 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.006 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 606) hydrogen bonds : angle 3.74870 ( 1780) metal coordination : bond 0.00457 ( 16) metal coordination : angle 3.04634 ( 21) covalent geometry : bond 0.00277 (17332) covalent geometry : angle 0.54881 (23627) *********************** 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 465 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 161 ASP cc_start: 0.7056 (m-30) cc_final: 0.6487 (t0) REVERT: C 164 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6453 (tm-30) REVERT: C 187 LEU cc_start: 0.7632 (tp) cc_final: 0.7354 (tp) REVERT: C 218 LYS cc_start: 0.8015 (tptt) cc_final: 0.7718 (mtmm) REVERT: C 249 THR cc_start: 0.8480 (p) cc_final: 0.8271 (t) REVERT: C 250 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (tt) REVERT: C 267 LYS cc_start: 0.8240 (mttp) cc_final: 0.7931 (mmmm) REVERT: C 273 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7932 (mtp85) REVERT: C 326 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8483 (mm) REVERT: C 354 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8444 (m) REVERT: C 400 TRP cc_start: 0.8678 (m100) cc_final: 0.8447 (m100) REVERT: C 508 LYS cc_start: 0.8131 (tppt) cc_final: 0.7737 (mmtm) REVERT: C 585 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7620 (m90) REVERT: C 599 LYS cc_start: 0.8097 (tppt) cc_final: 0.7676 (ttmm) REVERT: C 688 GLN cc_start: 0.8067 (mt0) cc_final: 0.7701 (mt0) REVERT: B 95 ASP cc_start: 0.7576 (t0) cc_final: 0.7325 (t0) REVERT: B 142 VAL cc_start: 0.7869 (t) cc_final: 0.7517 (m) REVERT: B 171 ASP cc_start: 0.7609 (p0) cc_final: 0.7293 (p0) REVERT: B 178 LEU cc_start: 0.8804 (mt) cc_final: 0.8554 (mp) REVERT: B 313 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (mtmt) REVERT: B 454 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 617 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7649 (mmtt) REVERT: B 717 GLU cc_start: 0.7453 (pm20) cc_final: 0.7017 (pm20) REVERT: B 744 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7719 (mtmt) REVERT: B 752 CYS cc_start: 0.6992 (p) cc_final: 0.6274 (p) REVERT: B 847 ASP cc_start: 0.7620 (p0) cc_final: 0.7399 (t0) REVERT: B 933 VAL cc_start: 0.8488 (t) cc_final: 0.8218 (m) REVERT: B 973 ASN cc_start: 0.8128 (p0) cc_final: 0.7808 (p0) REVERT: B 1496 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 1557 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 1593 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8043 (mtpp) outliers start: 78 outliers final: 59 residues processed: 426 average time/residue: 0.3414 time to fit residues: 208.3462 Evaluate side-chains 448 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 382 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 136 ASP 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 326 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL 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 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 630 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 451 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS 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 719 ARG Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU 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 968 ASP 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 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 1598 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 90 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107984 restraints weight = 24363.076| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.97 r_work: 0.3206 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17348 Z= 0.143 Angle : 0.580 9.902 23648 Z= 0.297 Chirality : 0.042 0.223 2566 Planarity : 0.005 0.067 2844 Dihedral : 15.249 179.724 2933 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.11 % Allowed : 25.22 % Favored : 70.67 % 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: 1.80 (0.20), residues: 635 sheet: 0.32 (0.33), residues: 251 loop : -1.36 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.021 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.005 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 606) hydrogen bonds : angle 3.74133 ( 1780) metal coordination : bond 0.00741 ( 16) metal coordination : angle 3.83040 ( 21) covalent geometry : bond 0.00335 (17332) covalent geometry : angle 0.56878 (23627) ********************** 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 451 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7082 (m-30) cc_final: 0.6495 (t0) REVERT: C 164 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6480 (tm-30) REVERT: C 187 LEU cc_start: 0.7585 (tp) cc_final: 0.7313 (tp) REVERT: C 218 LYS cc_start: 0.8011 (tptt) cc_final: 0.7710 (mtmm) REVERT: C 249 THR cc_start: 0.8481 (p) cc_final: 0.8270 (t) REVERT: C 250 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (tt) REVERT: C 267 LYS cc_start: 0.8289 (mttp) cc_final: 0.7971 (mmmm) REVERT: C 273 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7926 (mtp85) REVERT: C 354 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8442 (m) REVERT: C 400 TRP cc_start: 0.8664 (m100) cc_final: 0.8421 (m100) REVERT: C 508 LYS cc_start: 0.8185 (tppt) cc_final: 0.7789 (mmtm) REVERT: C 585 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7625 (m90) REVERT: C 599 LYS cc_start: 0.8077 (tppt) cc_final: 0.7666 (ttmm) REVERT: C 628 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6712 (mt-10) REVERT: C 688 GLN cc_start: 0.8095 (mt0) cc_final: 0.7720 (mt0) REVERT: B 95 ASP cc_start: 0.7603 (t0) cc_final: 0.7346 (t0) REVERT: B 142 VAL cc_start: 0.7879 (t) cc_final: 0.7514 (m) REVERT: B 171 ASP cc_start: 0.7612 (p0) cc_final: 0.7310 (p0) REVERT: B 178 LEU cc_start: 0.8811 (mt) cc_final: 0.8561 (mp) REVERT: B 313 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7532 (mtmt) REVERT: B 454 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 633 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: B 717 GLU cc_start: 0.7415 (pm20) cc_final: 0.6973 (pm20) REVERT: B 744 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7676 (mtmt) REVERT: B 752 CYS cc_start: 0.6953 (p) cc_final: 0.6220 (p) REVERT: B 933 VAL cc_start: 0.8479 (t) cc_final: 0.8210 (m) REVERT: B 973 ASN cc_start: 0.8110 (p0) cc_final: 0.7785 (p0) REVERT: B 1496 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 1557 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7844 (t80) REVERT: B 1593 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8055 (mtpp) outliers start: 70 outliers final: 58 residues processed: 414 average time/residue: 0.3394 time to fit residues: 201.2385 Evaluate side-chains 443 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 379 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 136 ASP 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 354 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL 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 560 SER Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 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 451 VAL Chi-restraints excluded: chain B residue 540 VAL 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 719 ARG 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 909 GLN Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 968 ASP 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 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1598 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 154 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 195 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 0.0370 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 134 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108610 restraints weight = 24257.809| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.09 r_work: 0.3213 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17348 Z= 0.109 Angle : 0.564 7.170 23648 Z= 0.290 Chirality : 0.040 0.248 2566 Planarity : 0.005 0.067 2844 Dihedral : 15.223 179.288 2933 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.99 % Allowed : 25.51 % Favored : 70.50 % 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: 0.03 (0.19), residues: 1924 helix: 1.89 (0.20), residues: 635 sheet: 0.32 (0.33), residues: 251 loop : -1.33 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.022 0.001 PHE C 491 TYR 0.019 0.001 TYR B 202 ARG 0.005 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 606) hydrogen bonds : angle 3.69039 ( 1780) metal coordination : bond 0.00492 ( 16) metal coordination : angle 3.32473 ( 21) covalent geometry : bond 0.00248 (17332) covalent geometry : angle 0.55557 (23627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9555.34 seconds wall clock time: 164 minutes 14.55 seconds (9854.55 seconds total)