Starting phenix.real_space_refine on Fri Feb 14 23:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845.map" model { file = "/net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yud_6845/02_2025/5yud_6845_neut.cif" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 44 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 C 6691 2.51 5 N 1779 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10510 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9943 Classifications: {'peptide': 1238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1187} Chain breaks: 1 Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 536 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.13, per 1000 atoms: 0.58 Number of scatterers: 10510 At special positions: 0 Unit cell: (92.7643, 118.895, 138.493, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 3 15.00 O 1983 8.00 N 1779 7.00 C 6691 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 9 sheets defined 48.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 22 through 25 removed outlier: 3.820A pdb=" N ALA A 25 " --> pdb=" O GLU A 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 25' Processing helix chain 'A' and resid 26 through 31 removed outlier: 4.056A pdb=" N ASP A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.807A pdb=" N GLU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.680A pdb=" N THR A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.728A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.725A pdb=" N ARG A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.376A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.649A pdb=" N ARG A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.656A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 removed outlier: 5.303A pdb=" N ALA A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.110A pdb=" N ALA A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 removed outlier: 3.856A pdb=" N ASN A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.711A pdb=" N SER A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.922A pdb=" N LEU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 4.178A pdb=" N TYR A 496 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 498' Processing helix chain 'A' and resid 516 through 524 removed outlier: 4.604A pdb=" N GLN A 522 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.543A pdb=" N LEU A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.174A pdb=" N ILE A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.819A pdb=" N THR A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.971A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.803A pdb=" N GLY A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.729A pdb=" N VAL A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.696A pdb=" N GLN A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 703 removed outlier: 3.581A pdb=" N GLN A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.993A pdb=" N GLU A 722 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.898A pdb=" N LEU A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 728' Processing helix chain 'A' and resid 745 through 760 removed outlier: 3.755A pdb=" N ALA A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.798A pdb=" N ARG A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.629A pdb=" N ALA A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 3.549A pdb=" N TYR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 800 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 removed outlier: 4.420A pdb=" N THR A 807 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 836 through 852 removed outlier: 4.009A pdb=" N LEU A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 873 removed outlier: 3.764A pdb=" N SER A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 removed outlier: 4.165A pdb=" N PHE A 884 " --> pdb=" O GLU A 880 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 887 " --> pdb=" O PRO A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.268A pdb=" N ASN A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.757A pdb=" N TYR A 932 " --> pdb=" O TYR A 929 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 937 " --> pdb=" O PHE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 978 removed outlier: 3.923A pdb=" N ILE A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 978 " --> pdb=" O TYR A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 1008 through 1012 removed outlier: 3.862A pdb=" N ALA A1011 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.932A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1025 " --> pdb=" O MET A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1049 removed outlier: 3.884A pdb=" N SER A1043 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Proline residue: A1046 - end of helix Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.681A pdb=" N LEU A1076 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1154 removed outlier: 4.114A pdb=" N GLN A1152 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A1153 " --> pdb=" O LYS A1149 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A1154 " --> pdb=" O PHE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1157 No H-bonds generated for 'chain 'A' and resid 1155 through 1157' Processing helix chain 'A' and resid 1173 through 1178 Processing helix chain 'A' and resid 1201 through 1205 removed outlier: 3.969A pdb=" N PHE A1205 " --> pdb=" O LEU A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1234 Processing helix chain 'A' and resid 1247 through 1252 removed outlier: 4.030A pdb=" N GLN A1250 " --> pdb=" O GLY A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1258 removed outlier: 3.616A pdb=" N GLN A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1262 Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.836A pdb=" N LYS A1344 " --> pdb=" O ALA A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1351 Processing helix chain 'A' and resid 1364 through 1374 Processing helix chain 'A' and resid 1397 through 1402 Processing helix chain 'C' and resid 426 through 444 removed outlier: 4.757A pdb=" N ASN C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 483 removed outlier: 4.068A pdb=" N GLU C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.923A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470 removed outlier: 6.647A pdb=" N PHE A 548 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA A 580 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 550 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS A 582 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 551 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AA6, first strand: chain 'A' and resid 892 through 895 removed outlier: 5.878A pdb=" N LYS A 892 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER A 916 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 894 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS A 918 " --> pdb=" O LEU A 894 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A 913 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N GLU A1003 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 915 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLN A1005 " --> pdb=" O ARG A 915 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 917 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE A 999 " --> pdb=" O GLN A1028 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A1030 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LYS A1001 " --> pdb=" O ILE A1030 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 892 through 895 removed outlier: 5.878A pdb=" N LYS A 892 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER A 916 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 894 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS A 918 " --> pdb=" O LEU A 894 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A 913 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N GLU A1003 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 915 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLN A1005 " --> pdb=" O ARG A 915 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 917 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A1032 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYS A1058 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1134 through 1135 removed outlier: 6.627A pdb=" N LEU A1134 " --> pdb=" O LYS A1163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1296 through 1299 314 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1766 1.31 - 1.44: 2799 1.44 - 1.56: 6082 1.56 - 1.69: 5 1.69 - 1.81: 75 Bond restraints: 10727 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C TRP A 76 " pdb=" N THR A 77 " ideal model delta sigma weight residual 1.331 1.190 0.141 2.07e-02 2.33e+03 4.63e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.25e+01 ... (remaining 10722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.51: 14398 5.51 - 11.01: 105 11.01 - 16.52: 6 16.52 - 22.03: 1 22.03 - 27.53: 3 Bond angle restraints: 14513 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 112.34 27.53 1.00e+00 1.00e+00 7.58e+02 angle pdb=" C HIS A 907 " pdb=" N PRO A 908 " pdb=" CA PRO A 908 " ideal model delta sigma weight residual 119.84 94.12 25.72 1.25e+00 6.40e-01 4.23e+02 angle pdb=" N TYR A 903 " pdb=" CA TYR A 903 " pdb=" C TYR A 903 " ideal model delta sigma weight residual 113.41 90.76 22.65 1.22e+00 6.72e-01 3.45e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.36 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.70 8.10 1.00e+00 1.00e+00 6.56e+01 ... (remaining 14508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 6084 15.98 - 31.97: 398 31.97 - 47.95: 37 47.95 - 63.93: 9 63.93 - 79.92: 5 Dihedral angle restraints: 6533 sinusoidal: 2677 harmonic: 3856 Sorted by residual: dihedral pdb=" CA HIS A1381 " pdb=" C HIS A1381 " pdb=" N PRO A1382 " pdb=" CA PRO A1382 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA GLN A 735 " pdb=" C GLN A 735 " pdb=" N ARG A 736 " pdb=" CA ARG A 736 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA GLU A1141 " pdb=" C GLU A1141 " pdb=" N SER A1142 " pdb=" CA SER A1142 " ideal model delta harmonic sigma weight residual -180.00 -145.39 -34.61 0 5.00e+00 4.00e-02 4.79e+01 ... (remaining 6530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1462 0.095 - 0.191: 159 0.191 - 0.286: 6 0.286 - 0.381: 0 0.381 - 0.477: 3 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA ASP A 947 " pdb=" N ASP A 947 " pdb=" C ASP A 947 " pdb=" CB ASP A 947 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA TYR A 903 " pdb=" N TYR A 903 " pdb=" C TYR A 903 " pdb=" CB TYR A 903 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ILE A1273 " pdb=" N ILE A1273 " pdb=" C ILE A1273 " pdb=" CB ILE A1273 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 1627 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 902 " -0.027 2.00e-02 2.50e+03 5.69e-02 3.23e+01 pdb=" C GLN A 902 " 0.098 2.00e-02 2.50e+03 pdb=" O GLN A 902 " -0.039 2.00e-02 2.50e+03 pdb=" N TYR A 903 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 907 " -0.095 5.00e-02 4.00e+02 1.40e-01 3.16e+01 pdb=" N PRO A 908 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 947 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C ASP A 947 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP A 947 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 948 " 0.025 2.00e-02 2.50e+03 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 11 2.02 - 2.74: 1716 2.74 - 3.46: 16973 3.46 - 4.18: 25772 4.18 - 4.90: 42157 Nonbonded interactions: 86629 Sorted by model distance: nonbonded pdb=" O ASP A 631 " pdb=" CD2 LEU A 635 " model vdw 1.301 3.460 nonbonded pdb=" OG SER A 59 " pdb=" CG1 VAL A 132 " model vdw 1.800 3.460 nonbonded pdb=" CD2 LEU A1274 " pdb=" CD1 ILE A1299 " model vdw 1.821 3.880 nonbonded pdb=" SG CYS A 467 " pdb=" CD2 LEU A 593 " model vdw 1.889 3.820 nonbonded pdb=" O ASP A 947 " pdb=" N TYR A 950 " model vdw 1.932 3.120 ... (remaining 86624 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.008 0.141 10727 Z= 0.547 Angle : 1.307 27.532 14513 Z= 0.782 Chirality : 0.060 0.477 1630 Planarity : 0.007 0.140 1865 Dihedral : 10.622 79.916 4023 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 55.14 Ramachandran Plot: Outliers : 1.07 % Allowed : 16.14 % Favored : 82.79 % Rotamer: Outliers : 0.17 % Allowed : 0.68 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.48 % 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: -5.50 (0.17), residues: 1307 helix: -4.49 (0.12), residues: 424 sheet: -3.01 (0.53), residues: 65 loop : -3.40 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 76 HIS 0.012 0.003 HIS A 88 PHE 0.031 0.004 PHE A1154 TYR 0.055 0.003 TYR A 950 ARG 0.018 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.9298 (mttt) cc_final: 0.8991 (mtpt) REVERT: A 220 TRP cc_start: 0.8741 (m100) cc_final: 0.8461 (m100) REVERT: A 418 HIS cc_start: 0.8442 (m-70) cc_final: 0.8143 (m-70) REVERT: A 454 THR cc_start: 0.8189 (p) cc_final: 0.6872 (p) REVERT: A 548 PHE cc_start: 0.8310 (m-80) cc_final: 0.7993 (m-10) REVERT: A 967 ASP cc_start: 0.9120 (m-30) cc_final: 0.8538 (m-30) REVERT: A 1063 LEU cc_start: 0.8598 (tp) cc_final: 0.8308 (tp) REVERT: A 1123 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6558 (ptp90) REVERT: A 1223 THR cc_start: 0.9079 (m) cc_final: 0.8615 (m) REVERT: A 1226 LYS cc_start: 0.9434 (mttt) cc_final: 0.9058 (mmtm) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.3058 time to fit residues: 151.4855 Evaluate side-chains 239 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 88 HIS A 174 HIS A 206 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN A1261 GLN A1296 ASN A1322 ASN ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.080311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067032 restraints weight = 46395.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069117 restraints weight = 30552.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070650 restraints weight = 22127.271| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10727 Z= 0.296 Angle : 0.946 13.594 14513 Z= 0.485 Chirality : 0.052 0.328 1630 Planarity : 0.006 0.044 1865 Dihedral : 10.336 79.182 1446 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.25 % Favored : 88.29 % Rotamer: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.24 % 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: -3.98 (0.20), residues: 1307 helix: -2.36 (0.19), residues: 493 sheet: -3.31 (0.46), residues: 84 loop : -2.83 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 214 HIS 0.010 0.002 HIS A 582 PHE 0.018 0.002 PHE A1291 TYR 0.053 0.003 TYR A 950 ARG 0.007 0.001 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8186 (m-10) cc_final: 0.7579 (m-10) REVERT: A 68 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 96 GLN cc_start: 0.8751 (tt0) cc_final: 0.8292 (tm-30) REVERT: A 220 TRP cc_start: 0.8532 (m100) cc_final: 0.8236 (m100) REVERT: A 418 HIS cc_start: 0.8176 (m90) cc_final: 0.7975 (m90) REVERT: A 437 ASP cc_start: 0.8460 (m-30) cc_final: 0.8206 (m-30) REVERT: A 550 LEU cc_start: 0.8486 (mp) cc_final: 0.8197 (mp) REVERT: A 552 ASP cc_start: 0.6115 (t0) cc_final: 0.5405 (m-30) REVERT: A 553 TYR cc_start: 0.8055 (p90) cc_final: 0.7563 (p90) REVERT: A 635 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 749 GLN cc_start: 0.9069 (tt0) cc_final: 0.8525 (tp40) REVERT: A 795 TYR cc_start: 0.8747 (m-10) cc_final: 0.8447 (m-10) REVERT: A 885 ILE cc_start: 0.9655 (mt) cc_final: 0.9446 (tp) REVERT: A 967 ASP cc_start: 0.9287 (m-30) cc_final: 0.9072 (m-30) REVERT: A 977 ILE cc_start: 0.9734 (mt) cc_final: 0.9460 (tp) REVERT: A 1024 PHE cc_start: 0.9343 (m-10) cc_final: 0.8958 (m-80) REVERT: A 1041 LEU cc_start: 0.9746 (mm) cc_final: 0.9310 (tt) REVERT: A 1208 LEU cc_start: 0.8620 (mt) cc_final: 0.8401 (mt) REVERT: A 1239 GLU cc_start: 0.9321 (pt0) cc_final: 0.8405 (pt0) REVERT: A 1335 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7761 (mtp180) REVERT: A 1368 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8394 (tp30) REVERT: A 1369 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8924 (tt0) REVERT: A 1389 ILE cc_start: 0.8272 (mt) cc_final: 0.7743 (mt) REVERT: C 429 LEU cc_start: 0.9333 (tp) cc_final: 0.9087 (tp) REVERT: C 432 ASN cc_start: 0.9625 (m-40) cc_final: 0.9126 (m110) REVERT: C 454 ILE cc_start: 0.9308 (pt) cc_final: 0.9067 (mm) REVERT: C 456 ASP cc_start: 0.9112 (t0) cc_final: 0.8722 (t0) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2919 time to fit residues: 124.3227 Evaluate side-chains 239 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 228 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 663 GLN A 790 ASN A 843 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN A1099 HIS A1130 HIS A1315 GLN ** A1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1337 GLN ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.063467 restraints weight = 48631.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065502 restraints weight = 31366.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066935 restraints weight = 22398.872| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10727 Z= 0.429 Angle : 0.972 14.057 14513 Z= 0.495 Chirality : 0.051 0.253 1630 Planarity : 0.010 0.322 1865 Dihedral : 10.442 87.492 1446 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.78 % Favored : 86.69 % Rotamer: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.24 % 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: -3.89 (0.20), residues: 1307 helix: -1.89 (0.20), residues: 514 sheet: -3.44 (0.40), residues: 106 loop : -3.05 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 214 HIS 0.014 0.002 HIS A 582 PHE 0.028 0.003 PHE A1227 TYR 0.044 0.003 TYR A 950 ARG 0.007 0.001 ARG A1257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9269 (mtmm) REVERT: A 68 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 77 THR cc_start: 0.9430 (m) cc_final: 0.9021 (p) REVERT: A 96 GLN cc_start: 0.8697 (tt0) cc_final: 0.8200 (tp-100) REVERT: A 148 MET cc_start: 0.8153 (mmt) cc_final: 0.7923 (mmt) REVERT: A 216 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8649 (mm-30) REVERT: A 417 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7726 (mtt180) REVERT: A 476 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8934 (mtmm) REVERT: A 479 PHE cc_start: 0.9586 (t80) cc_final: 0.9364 (t80) REVERT: A 552 ASP cc_start: 0.6663 (t0) cc_final: 0.5432 (m-30) REVERT: A 553 TYR cc_start: 0.8061 (p90) cc_final: 0.7490 (p90) REVERT: A 795 TYR cc_start: 0.8743 (m-10) cc_final: 0.8262 (m-10) REVERT: A 967 ASP cc_start: 0.9338 (m-30) cc_final: 0.9136 (m-30) REVERT: A 1024 PHE cc_start: 0.9360 (m-10) cc_final: 0.9113 (m-80) REVERT: A 1238 GLU cc_start: 0.8172 (pt0) cc_final: 0.7958 (pt0) REVERT: A 1270 PHE cc_start: 0.8959 (m-80) cc_final: 0.8700 (m-10) REVERT: A 1281 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 1335 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7891 (mtm180) REVERT: A 1356 LEU cc_start: 0.8960 (tt) cc_final: 0.8697 (tt) REVERT: A 1358 ARG cc_start: 0.7910 (mpp80) cc_final: 0.7587 (mpp80) REVERT: A 1371 MET cc_start: 0.8993 (mtm) cc_final: 0.8763 (mtp) REVERT: A 1389 ILE cc_start: 0.8296 (mt) cc_final: 0.7987 (mt) REVERT: C 432 ASN cc_start: 0.9572 (m-40) cc_final: 0.9086 (m110) REVERT: C 456 ASP cc_start: 0.9107 (t0) cc_final: 0.8773 (t0) REVERT: C 463 VAL cc_start: 0.9467 (t) cc_final: 0.9265 (t) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2855 time to fit residues: 106.4349 Evaluate side-chains 203 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 0.0060 chunk 14 optimal weight: 10.0000 chunk 93 optimal weight: 0.0010 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 206 ASN A 228 GLN A 418 HIS ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 790 ASN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068010 restraints weight = 46219.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070152 restraints weight = 30361.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071710 restraints weight = 21895.261| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10727 Z= 0.219 Angle : 0.826 12.314 14513 Z= 0.414 Chirality : 0.047 0.278 1630 Planarity : 0.005 0.064 1865 Dihedral : 9.820 76.251 1446 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.86 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -3.35 (0.21), residues: 1307 helix: -1.36 (0.21), residues: 517 sheet: -3.27 (0.42), residues: 108 loop : -2.79 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.009 0.002 HIS A 582 PHE 0.024 0.002 PHE A1035 TYR 0.054 0.002 TYR A 950 ARG 0.009 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.9159 (tp) cc_final: 0.8685 (tt) REVERT: A 49 MET cc_start: 0.8489 (mpp) cc_final: 0.8222 (mpp) REVERT: A 77 THR cc_start: 0.9439 (m) cc_final: 0.9205 (p) REVERT: A 96 GLN cc_start: 0.8570 (tt0) cc_final: 0.8070 (tp-100) REVERT: A 97 CYS cc_start: 0.5834 (m) cc_final: 0.5385 (m) REVERT: A 239 TYR cc_start: 0.8470 (m-80) cc_final: 0.8085 (m-80) REVERT: A 418 HIS cc_start: 0.8433 (m90) cc_final: 0.8190 (m-70) REVERT: A 476 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8680 (mtmm) REVERT: A 479 PHE cc_start: 0.9601 (t80) cc_final: 0.9365 (t80) REVERT: A 537 SER cc_start: 0.9314 (m) cc_final: 0.9040 (p) REVERT: A 550 LEU cc_start: 0.8438 (mp) cc_final: 0.8192 (mp) REVERT: A 552 ASP cc_start: 0.6200 (t0) cc_final: 0.4987 (m-30) REVERT: A 597 LEU cc_start: 0.8906 (mt) cc_final: 0.8464 (mt) REVERT: A 628 TYR cc_start: 0.8876 (m-10) cc_final: 0.8615 (m-10) REVERT: A 768 ASP cc_start: 0.9088 (t0) cc_final: 0.8794 (t0) REVERT: A 941 LEU cc_start: 0.9166 (pt) cc_final: 0.8628 (pp) REVERT: A 1024 PHE cc_start: 0.9383 (m-10) cc_final: 0.9104 (m-80) REVERT: A 1114 LYS cc_start: 0.8962 (mttt) cc_final: 0.8418 (tttt) REVERT: A 1276 ASP cc_start: 0.8919 (t0) cc_final: 0.8667 (t70) REVERT: A 1314 PHE cc_start: 0.8586 (m-10) cc_final: 0.8347 (m-10) REVERT: A 1348 GLN cc_start: 0.5687 (mt0) cc_final: 0.5457 (pt0) REVERT: A 1389 ILE cc_start: 0.8148 (mt) cc_final: 0.7852 (mt) REVERT: C 432 ASN cc_start: 0.9614 (m-40) cc_final: 0.9097 (m110) REVERT: C 463 VAL cc_start: 0.9456 (t) cc_final: 0.9189 (t) REVERT: C 473 GLN cc_start: 0.8889 (mp10) cc_final: 0.8555 (mp10) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2933 time to fit residues: 115.6603 Evaluate side-chains 215 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN C 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065528 restraints weight = 46582.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067577 restraints weight = 30388.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069073 restraints weight = 21976.108| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10727 Z= 0.264 Angle : 0.814 12.351 14513 Z= 0.408 Chirality : 0.047 0.278 1630 Planarity : 0.005 0.102 1865 Dihedral : 9.607 79.001 1446 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.40 % Favored : 87.99 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -3.15 (0.22), residues: 1307 helix: -1.12 (0.21), residues: 527 sheet: -3.35 (0.46), residues: 98 loop : -2.75 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.005 0.001 HIS A 799 PHE 0.021 0.002 PHE A 954 TYR 0.042 0.002 TYR A 950 ARG 0.032 0.001 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8919 (mttt) cc_final: 0.8676 (mmmt) REVERT: A 49 MET cc_start: 0.8552 (mpp) cc_final: 0.8239 (mpp) REVERT: A 62 LYS cc_start: 0.9513 (mmmt) cc_final: 0.9184 (mtmm) REVERT: A 63 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7366 (mtt-85) REVERT: A 64 LEU cc_start: 0.9640 (mm) cc_final: 0.9366 (mm) REVERT: A 65 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8757 (mmmm) REVERT: A 68 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 77 THR cc_start: 0.9467 (m) cc_final: 0.9162 (p) REVERT: A 96 GLN cc_start: 0.8676 (tt0) cc_final: 0.7932 (tp-100) REVERT: A 216 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8579 (mm-30) REVERT: A 418 HIS cc_start: 0.8491 (m90) cc_final: 0.8209 (m-70) REVERT: A 476 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8659 (mtmm) REVERT: A 479 PHE cc_start: 0.9582 (t80) cc_final: 0.9332 (t80) REVERT: A 537 SER cc_start: 0.9251 (m) cc_final: 0.8946 (p) REVERT: A 543 GLN cc_start: 0.7900 (pp30) cc_final: 0.7526 (pp30) REVERT: A 550 LEU cc_start: 0.8532 (mp) cc_final: 0.8106 (mp) REVERT: A 552 ASP cc_start: 0.6255 (t0) cc_final: 0.4780 (m-30) REVERT: A 628 TYR cc_start: 0.8926 (m-10) cc_final: 0.8672 (m-10) REVERT: A 635 LEU cc_start: 0.8676 (pp) cc_final: 0.8321 (pp) REVERT: A 825 MET cc_start: 0.6193 (mtt) cc_final: 0.5275 (mtt) REVERT: A 830 ASP cc_start: 0.8998 (p0) cc_final: 0.8778 (p0) REVERT: A 941 LEU cc_start: 0.9248 (pt) cc_final: 0.8691 (pp) REVERT: A 1024 PHE cc_start: 0.9422 (m-10) cc_final: 0.9059 (m-80) REVERT: A 1102 LEU cc_start: 0.9242 (mt) cc_final: 0.9019 (mt) REVERT: A 1239 GLU cc_start: 0.9132 (pm20) cc_final: 0.8793 (pm20) REVERT: A 1276 ASP cc_start: 0.8901 (t0) cc_final: 0.8683 (t70) REVERT: A 1335 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7698 (mtp180) REVERT: A 1389 ILE cc_start: 0.8306 (mt) cc_final: 0.8048 (mt) REVERT: C 432 ASN cc_start: 0.9570 (m-40) cc_final: 0.9117 (m110) REVERT: C 455 GLU cc_start: 0.8851 (mp0) cc_final: 0.8423 (mp0) REVERT: C 456 ASP cc_start: 0.8801 (t0) cc_final: 0.8420 (t0) REVERT: C 463 VAL cc_start: 0.9462 (t) cc_final: 0.9205 (t) REVERT: C 473 GLN cc_start: 0.8924 (mp10) cc_final: 0.8625 (mp10) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2659 time to fit residues: 99.4989 Evaluate side-chains 203 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN C 441 GLN C 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066508 restraints weight = 46386.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068619 restraints weight = 30143.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070120 restraints weight = 21698.381| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10727 Z= 0.248 Angle : 0.825 12.063 14513 Z= 0.410 Chirality : 0.048 0.244 1630 Planarity : 0.006 0.106 1865 Dihedral : 9.475 81.899 1446 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.25 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.99 (0.22), residues: 1307 helix: -0.94 (0.22), residues: 518 sheet: -3.30 (0.43), residues: 108 loop : -2.66 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.007 0.001 HIS A 799 PHE 0.027 0.002 PHE A1035 TYR 0.032 0.002 TYR A 950 ARG 0.017 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8541 (mpp) cc_final: 0.8138 (mpp) REVERT: A 64 LEU cc_start: 0.9416 (mm) cc_final: 0.9139 (mm) REVERT: A 65 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8947 (mmmm) REVERT: A 68 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 77 THR cc_start: 0.9482 (m) cc_final: 0.9143 (p) REVERT: A 96 GLN cc_start: 0.8384 (tt0) cc_final: 0.7967 (tp40) REVERT: A 115 GLU cc_start: 0.9150 (tt0) cc_final: 0.8876 (tt0) REVERT: A 418 HIS cc_start: 0.8542 (m90) cc_final: 0.8228 (m-70) REVERT: A 476 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8696 (mtmm) REVERT: A 479 PHE cc_start: 0.9578 (t80) cc_final: 0.9345 (t80) REVERT: A 550 LEU cc_start: 0.8506 (mp) cc_final: 0.8149 (mp) REVERT: A 552 ASP cc_start: 0.6303 (t0) cc_final: 0.4758 (m-30) REVERT: A 628 TYR cc_start: 0.8964 (m-10) cc_final: 0.8667 (m-10) REVERT: A 635 LEU cc_start: 0.8458 (pp) cc_final: 0.8010 (pp) REVERT: A 825 MET cc_start: 0.6334 (mtt) cc_final: 0.5271 (mtt) REVERT: A 830 ASP cc_start: 0.8933 (p0) cc_final: 0.8693 (p0) REVERT: A 941 LEU cc_start: 0.9219 (pt) cc_final: 0.8583 (pp) REVERT: A 1024 PHE cc_start: 0.9358 (m-10) cc_final: 0.8961 (m-80) REVERT: A 1114 LYS cc_start: 0.9006 (mttt) cc_final: 0.8492 (tttt) REVERT: A 1239 GLU cc_start: 0.9040 (pm20) cc_final: 0.8656 (pm20) REVERT: A 1276 ASP cc_start: 0.8830 (t0) cc_final: 0.8490 (t70) REVERT: A 1281 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8431 (mt-10) REVERT: A 1335 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7523 (mtp180) REVERT: C 455 GLU cc_start: 0.8798 (mp0) cc_final: 0.8417 (mp0) REVERT: C 456 ASP cc_start: 0.8868 (t0) cc_final: 0.8484 (t0) REVERT: C 463 VAL cc_start: 0.9468 (t) cc_final: 0.9205 (t) REVERT: C 473 GLN cc_start: 0.8874 (mp10) cc_final: 0.8592 (mp10) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2616 time to fit residues: 96.0855 Evaluate side-chains 209 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 116 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN C 441 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066699 restraints weight = 47013.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068867 restraints weight = 30245.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070448 restraints weight = 21612.522| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10727 Z= 0.244 Angle : 0.805 11.935 14513 Z= 0.403 Chirality : 0.047 0.250 1630 Planarity : 0.005 0.054 1865 Dihedral : 9.333 86.826 1446 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.01 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.74 (0.22), residues: 1307 helix: -0.70 (0.22), residues: 509 sheet: -3.40 (0.39), residues: 130 loop : -2.40 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.006 0.001 HIS A 799 PHE 0.017 0.002 PHE A 954 TYR 0.041 0.002 TYR A 950 ARG 0.008 0.001 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.9108 (m90) cc_final: 0.8766 (m90) REVERT: A 49 MET cc_start: 0.8427 (mpp) cc_final: 0.8132 (mpp) REVERT: A 65 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8873 (mmmm) REVERT: A 68 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 77 THR cc_start: 0.9517 (m) cc_final: 0.9214 (p) REVERT: A 96 GLN cc_start: 0.8353 (tt0) cc_final: 0.7777 (tp40) REVERT: A 97 CYS cc_start: 0.6247 (m) cc_final: 0.5749 (m) REVERT: A 115 GLU cc_start: 0.9182 (tt0) cc_final: 0.8891 (tt0) REVERT: A 407 LEU cc_start: 0.9360 (tp) cc_final: 0.8732 (tp) REVERT: A 418 HIS cc_start: 0.8607 (m90) cc_final: 0.8292 (m-70) REVERT: A 476 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8710 (mtmm) REVERT: A 550 LEU cc_start: 0.8412 (mp) cc_final: 0.8095 (mp) REVERT: A 552 ASP cc_start: 0.6451 (t0) cc_final: 0.4782 (m-30) REVERT: A 628 TYR cc_start: 0.8908 (m-10) cc_final: 0.8550 (m-10) REVERT: A 635 LEU cc_start: 0.8527 (pp) cc_final: 0.8012 (pp) REVERT: A 825 MET cc_start: 0.6254 (mtt) cc_final: 0.5928 (mtt) REVERT: A 941 LEU cc_start: 0.9244 (pt) cc_final: 0.8587 (pp) REVERT: A 1013 ASP cc_start: 0.8672 (m-30) cc_final: 0.8471 (m-30) REVERT: A 1024 PHE cc_start: 0.9380 (m-10) cc_final: 0.8998 (m-80) REVERT: A 1092 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8345 (tm-30) REVERT: A 1114 LYS cc_start: 0.8972 (mttt) cc_final: 0.8441 (tttt) REVERT: A 1196 MET cc_start: 0.8844 (ptp) cc_final: 0.8445 (mpp) REVERT: A 1239 GLU cc_start: 0.9009 (pm20) cc_final: 0.8701 (pm20) REVERT: A 1276 ASP cc_start: 0.8828 (t0) cc_final: 0.8507 (t70) REVERT: A 1335 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7467 (mtp180) REVERT: C 455 GLU cc_start: 0.8873 (mp0) cc_final: 0.8491 (mp0) REVERT: C 456 ASP cc_start: 0.8918 (t0) cc_final: 0.8518 (t0) REVERT: C 463 VAL cc_start: 0.9454 (t) cc_final: 0.9192 (t) REVERT: C 473 GLN cc_start: 0.8967 (mp10) cc_final: 0.8605 (mp10) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2665 time to fit residues: 94.4165 Evaluate side-chains 208 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 114 optimal weight: 0.0060 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1339 GLN A1348 GLN C 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069155 restraints weight = 45378.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071372 restraints weight = 29650.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072968 restraints weight = 21313.811| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10727 Z= 0.198 Angle : 0.785 11.135 14513 Z= 0.385 Chirality : 0.046 0.251 1630 Planarity : 0.004 0.053 1865 Dihedral : 9.064 87.994 1446 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.79 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.61 (0.23), residues: 1307 helix: -0.58 (0.23), residues: 512 sheet: -3.39 (0.40), residues: 118 loop : -2.37 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 220 HIS 0.005 0.001 HIS A 799 PHE 0.034 0.001 PHE A1035 TYR 0.037 0.002 TYR A 950 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8490 (mpp) cc_final: 0.8195 (mpp) REVERT: A 62 LYS cc_start: 0.9411 (mppt) cc_final: 0.9140 (mppt) REVERT: A 64 LEU cc_start: 0.9426 (mm) cc_final: 0.9040 (mm) REVERT: A 65 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8635 (mmmm) REVERT: A 68 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 96 GLN cc_start: 0.8345 (tt0) cc_final: 0.7876 (tp40) REVERT: A 115 GLU cc_start: 0.9160 (tt0) cc_final: 0.8898 (tt0) REVERT: A 220 TRP cc_start: 0.8222 (m100) cc_final: 0.7502 (m100) REVERT: A 407 LEU cc_start: 0.9127 (tp) cc_final: 0.8797 (tp) REVERT: A 418 HIS cc_start: 0.8462 (m90) cc_final: 0.8132 (m-70) REVERT: A 450 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8850 (tp40) REVERT: A 476 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8509 (mtmm) REVERT: A 628 TYR cc_start: 0.8843 (m-10) cc_final: 0.8407 (m-10) REVERT: A 635 LEU cc_start: 0.8423 (pp) cc_final: 0.7791 (pp) REVERT: A 825 MET cc_start: 0.6026 (mtt) cc_final: 0.5613 (mtt) REVERT: A 941 LEU cc_start: 0.9130 (pt) cc_final: 0.8376 (pp) REVERT: A 1024 PHE cc_start: 0.9403 (m-10) cc_final: 0.9013 (m-80) REVERT: A 1070 GLN cc_start: 0.9493 (mt0) cc_final: 0.9126 (mm-40) REVERT: A 1092 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8091 (tm-30) REVERT: A 1114 LYS cc_start: 0.8935 (mttt) cc_final: 0.8622 (tttt) REVERT: A 1123 ARG cc_start: 0.8160 (mtt180) cc_final: 0.6734 (ptp-170) REVERT: A 1196 MET cc_start: 0.8550 (ptp) cc_final: 0.8315 (ptp) REVERT: A 1239 GLU cc_start: 0.8893 (pm20) cc_final: 0.8540 (pm20) REVERT: A 1335 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7276 (mtp180) REVERT: A 1339 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8037 (mm110) REVERT: C 435 LYS cc_start: 0.9268 (tmtt) cc_final: 0.9052 (tmtt) REVERT: C 455 GLU cc_start: 0.8899 (mp0) cc_final: 0.8507 (mp0) REVERT: C 456 ASP cc_start: 0.8811 (t0) cc_final: 0.8450 (t0) REVERT: C 463 VAL cc_start: 0.9427 (t) cc_final: 0.9158 (t) REVERT: C 473 GLN cc_start: 0.8920 (mp10) cc_final: 0.8634 (mp10) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2656 time to fit residues: 95.7707 Evaluate side-chains 211 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 444 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067022 restraints weight = 46862.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.069181 restraints weight = 30526.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070707 restraints weight = 21969.861| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10727 Z= 0.254 Angle : 0.810 12.579 14513 Z= 0.402 Chirality : 0.047 0.238 1630 Planarity : 0.005 0.082 1865 Dihedral : 8.951 85.223 1446 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.63 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.53 (0.23), residues: 1307 helix: -0.45 (0.23), residues: 512 sheet: -3.49 (0.40), residues: 120 loop : -2.35 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 220 HIS 0.005 0.001 HIS A 799 PHE 0.024 0.002 PHE A1314 TYR 0.030 0.002 TYR A 950 ARG 0.012 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.9253 (m90) cc_final: 0.8950 (m90) REVERT: A 49 MET cc_start: 0.8506 (mpp) cc_final: 0.8225 (mpp) REVERT: A 62 LYS cc_start: 0.9433 (mppt) cc_final: 0.9201 (mppt) REVERT: A 96 GLN cc_start: 0.8475 (tt0) cc_final: 0.7986 (tp40) REVERT: A 115 GLU cc_start: 0.9197 (tt0) cc_final: 0.8947 (tt0) REVERT: A 418 HIS cc_start: 0.8459 (m90) cc_final: 0.8137 (m-70) REVERT: A 450 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8907 (tp40) REVERT: A 476 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8565 (mtmm) REVERT: A 628 TYR cc_start: 0.8899 (m-10) cc_final: 0.8507 (m-10) REVERT: A 635 LEU cc_start: 0.8473 (pp) cc_final: 0.7891 (pp) REVERT: A 825 MET cc_start: 0.6254 (mtt) cc_final: 0.5297 (mtm) REVERT: A 830 ASP cc_start: 0.8782 (p0) cc_final: 0.8574 (p0) REVERT: A 941 LEU cc_start: 0.9243 (pt) cc_final: 0.8557 (pp) REVERT: A 1024 PHE cc_start: 0.9420 (m-10) cc_final: 0.9035 (m-80) REVERT: A 1034 LEU cc_start: 0.7982 (mp) cc_final: 0.6767 (tt) REVERT: A 1070 GLN cc_start: 0.9500 (mt0) cc_final: 0.9272 (pt0) REVERT: A 1092 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8308 (tm-30) REVERT: A 1114 LYS cc_start: 0.8930 (mttt) cc_final: 0.8468 (tttt) REVERT: A 1123 ARG cc_start: 0.8218 (mtt180) cc_final: 0.6820 (ptp-170) REVERT: A 1196 MET cc_start: 0.8725 (ptp) cc_final: 0.8487 (ptp) REVERT: A 1210 ILE cc_start: 0.9484 (tp) cc_final: 0.9212 (tp) REVERT: A 1239 GLU cc_start: 0.8977 (pm20) cc_final: 0.7862 (pm20) REVERT: A 1335 ARG cc_start: 0.7584 (mtp180) cc_final: 0.7333 (mtp180) REVERT: C 435 LYS cc_start: 0.9279 (tmtt) cc_final: 0.9074 (tmtt) REVERT: C 437 ASP cc_start: 0.8892 (m-30) cc_final: 0.8630 (m-30) REVERT: C 455 GLU cc_start: 0.8915 (mp0) cc_final: 0.8546 (mp0) REVERT: C 456 ASP cc_start: 0.8861 (t0) cc_final: 0.8491 (t0) REVERT: C 463 VAL cc_start: 0.9445 (t) cc_final: 0.9197 (t) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2573 time to fit residues: 90.7224 Evaluate side-chains 204 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 72 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 0.0870 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN C 474 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069541 restraints weight = 45389.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071697 restraints weight = 29618.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073252 restraints weight = 21303.739| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10727 Z= 0.220 Angle : 0.808 12.086 14513 Z= 0.396 Chirality : 0.048 0.406 1630 Planarity : 0.005 0.049 1865 Dihedral : 8.807 82.824 1446 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.25 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.08 % 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: -2.62 (0.23), residues: 1307 helix: -0.54 (0.23), residues: 526 sheet: -3.48 (0.41), residues: 120 loop : -2.43 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 220 HIS 0.005 0.001 HIS A1360 PHE 0.041 0.002 PHE A1390 TYR 0.048 0.002 TYR A 950 ARG 0.013 0.001 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.9250 (m90) cc_final: 0.8902 (m90) REVERT: A 49 MET cc_start: 0.8553 (mpp) cc_final: 0.8222 (mpp) REVERT: A 62 LYS cc_start: 0.9409 (mppt) cc_final: 0.9159 (mppt) REVERT: A 96 GLN cc_start: 0.8422 (tt0) cc_final: 0.7984 (tp40) REVERT: A 115 GLU cc_start: 0.9159 (tt0) cc_final: 0.8885 (tt0) REVERT: A 220 TRP cc_start: 0.8258 (m100) cc_final: 0.7583 (m100) REVERT: A 407 LEU cc_start: 0.9278 (tp) cc_final: 0.8820 (tp) REVERT: A 418 HIS cc_start: 0.8325 (m90) cc_final: 0.7974 (m-70) REVERT: A 450 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8901 (tp40) REVERT: A 476 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8525 (mtmm) REVERT: A 628 TYR cc_start: 0.8882 (m-10) cc_final: 0.8565 (m-10) REVERT: A 635 LEU cc_start: 0.8387 (pp) cc_final: 0.7613 (pp) REVERT: A 825 MET cc_start: 0.6098 (mtt) cc_final: 0.5303 (mtm) REVERT: A 850 LEU cc_start: 0.9593 (tt) cc_final: 0.9376 (tp) REVERT: A 905 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8439 (ttm-80) REVERT: A 941 LEU cc_start: 0.9203 (pt) cc_final: 0.8514 (pp) REVERT: A 967 ASP cc_start: 0.9350 (m-30) cc_final: 0.9100 (m-30) REVERT: A 1024 PHE cc_start: 0.9416 (m-10) cc_final: 0.9022 (m-80) REVERT: A 1034 LEU cc_start: 0.7856 (mp) cc_final: 0.6784 (tt) REVERT: A 1070 GLN cc_start: 0.9496 (mt0) cc_final: 0.9266 (pt0) REVERT: A 1092 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8222 (tm-30) REVERT: A 1114 LYS cc_start: 0.8918 (mttt) cc_final: 0.8549 (tttt) REVERT: A 1123 ARG cc_start: 0.8216 (mtt180) cc_final: 0.6809 (ptp-170) REVERT: A 1196 MET cc_start: 0.8675 (ptp) cc_final: 0.8414 (ptp) REVERT: A 1339 GLN cc_start: 0.8569 (mm110) cc_final: 0.8335 (mm110) REVERT: A 1389 ILE cc_start: 0.7693 (mt) cc_final: 0.7480 (mt) REVERT: C 437 ASP cc_start: 0.8930 (m-30) cc_final: 0.8587 (m-30) REVERT: C 455 GLU cc_start: 0.8903 (mp0) cc_final: 0.8682 (mp0) REVERT: C 456 ASP cc_start: 0.8881 (t0) cc_final: 0.8591 (t0) REVERT: C 463 VAL cc_start: 0.9450 (t) cc_final: 0.9184 (t) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2667 time to fit residues: 96.8919 Evaluate side-chains 202 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 0.0170 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 463 ASN ** A 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN ** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN ** A1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.085062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071286 restraints weight = 44627.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073513 restraints weight = 29238.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075088 restraints weight = 21082.573| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10727 Z= 0.215 Angle : 0.811 11.689 14513 Z= 0.397 Chirality : 0.047 0.251 1630 Planarity : 0.004 0.050 1865 Dihedral : 8.668 81.006 1446 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.86 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.62 (0.23), residues: 1307 helix: -0.50 (0.23), residues: 534 sheet: -3.52 (0.41), residues: 126 loop : -2.47 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 220 HIS 0.010 0.001 HIS A1360 PHE 0.046 0.001 PHE A 954 TYR 0.072 0.002 TYR A 950 ARG 0.010 0.001 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.58 seconds wall clock time: 60 minutes 59.99 seconds (3659.99 seconds total)