Starting phenix.real_space_refine on Mon Jul 28 22:28:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yud_6845/07_2025/5yud_6845_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yud_6845/07_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_6845/07_2025/5yud_6845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yud_6845/07_2025/5yud_6845.map" model { file = "/net/cci-nas-00/data/ceres_data/5yud_6845/07_2025/5yud_6845_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yud_6845/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.30, per 1000 atoms: 0.60 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: 2.83 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: 1.25 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: 3.87 Time building geometry restraints manager: 3.35 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.080 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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 : 0.012 0.826 10728 Z= 0.904 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 Details of bonding type rmsd hydrogen bonds : bond 0.38109 ( 314) hydrogen bonds : angle 10.52314 ( 861) covalent geometry : bond 0.00838 (10727) covalent geometry : angle 1.30740 (14513) Misc. bond : bond 0.82599 ( 1) *********************** 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 : 1.298 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: 0.3502 time to fit residues: 173.4555 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 : 1.138 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.080301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067020 restraints weight = 46402.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069105 restraints weight = 30594.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070615 restraints weight = 22147.967| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 10728 Z= 0.213 Angle : 0.946 13.595 14513 Z= 0.485 Chirality : 0.052 0.328 1630 Planarity : 0.006 0.044 1865 Dihedral : 10.336 79.183 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 Details of bonding type rmsd hydrogen bonds : bond 0.07566 ( 314) hydrogen bonds : angle 7.43226 ( 861) covalent geometry : bond 0.00458 (10727) covalent geometry : angle 0.94592 (14513) Misc. bond : bond 0.00090 ( 1) *********************** 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 : 1.120 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: 0.8183 (m-10) cc_final: 0.7578 (m-10) REVERT: A 68 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 96 GLN cc_start: 0.8750 (tt0) cc_final: 0.8293 (tm-30) REVERT: A 220 TRP cc_start: 0.8533 (m100) cc_final: 0.8235 (m100) REVERT: A 437 ASP cc_start: 0.8449 (m-30) cc_final: 0.8196 (m-30) REVERT: A 550 LEU cc_start: 0.8489 (mp) cc_final: 0.8200 (mp) REVERT: A 552 ASP cc_start: 0.6109 (t0) cc_final: 0.5404 (m-30) REVERT: A 553 TYR cc_start: 0.8052 (p90) cc_final: 0.7562 (p90) REVERT: A 635 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 749 GLN cc_start: 0.9072 (tt0) cc_final: 0.8527 (tp40) REVERT: A 795 TYR cc_start: 0.8742 (m-10) cc_final: 0.8443 (m-10) REVERT: A 885 ILE cc_start: 0.9656 (mt) cc_final: 0.9445 (tp) REVERT: A 967 ASP cc_start: 0.9286 (m-30) cc_final: 0.9072 (m-30) REVERT: A 977 ILE cc_start: 0.9733 (mt) cc_final: 0.9459 (tp) REVERT: A 1024 PHE cc_start: 0.9341 (m-10) cc_final: 0.8956 (m-80) REVERT: A 1041 LEU cc_start: 0.9745 (mm) cc_final: 0.9310 (tt) REVERT: A 1208 LEU cc_start: 0.8619 (mt) cc_final: 0.8399 (mt) REVERT: A 1239 GLU cc_start: 0.9322 (pt0) cc_final: 0.8406 (pt0) REVERT: A 1335 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7757 (mtp180) REVERT: A 1368 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8393 (tp30) REVERT: A 1369 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8923 (tt0) REVERT: A 1389 ILE cc_start: 0.8273 (mt) cc_final: 0.7744 (mt) REVERT: C 429 LEU cc_start: 0.9328 (tp) cc_final: 0.9083 (tp) REVERT: C 432 ASN cc_start: 0.9625 (m-40) cc_final: 0.9127 (m110) REVERT: C 454 ILE cc_start: 0.9310 (pt) cc_final: 0.9068 (mm) REVERT: C 456 ASP cc_start: 0.9112 (t0) cc_final: 0.8721 (t0) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2861 time to fit residues: 122.1630 Evaluate side-chains 237 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 790 ASN A 843 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064370 restraints weight = 48502.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066419 restraints weight = 31251.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067905 restraints weight = 22304.071| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10728 Z= 0.275 Angle : 0.929 13.865 14513 Z= 0.474 Chirality : 0.050 0.252 1630 Planarity : 0.010 0.332 1865 Dihedral : 10.342 89.517 1446 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.62 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -3.78 (0.20), residues: 1307 helix: -1.87 (0.20), residues: 514 sheet: -3.39 (0.48), residues: 78 loop : -2.98 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 214 HIS 0.014 0.002 HIS A 582 PHE 0.026 0.003 PHE A1227 TYR 0.040 0.003 TYR A 950 ARG 0.007 0.001 ARG A1380 Details of bonding type rmsd hydrogen bonds : bond 0.06248 ( 314) hydrogen bonds : angle 7.15109 ( 861) covalent geometry : bond 0.00595 (10727) covalent geometry : angle 0.92865 (14513) Misc. bond : bond 0.00106 ( 1) *********************** 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 277 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.121 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 62 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9243 (mtmm) REVERT: A 68 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 77 THR cc_start: 0.9420 (m) cc_final: 0.9063 (p) REVERT: A 96 GLN cc_start: 0.8656 (tt0) cc_final: 0.8198 (tp-100) REVERT: A 148 MET cc_start: 0.8109 (mmt) cc_final: 0.7885 (mmt) REVERT: A 216 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 220 TRP cc_start: 0.8598 (m100) cc_final: 0.8305 (m-90) REVERT: A 437 ASP cc_start: 0.8439 (m-30) cc_final: 0.8228 (m-30) REVERT: A 479 PHE cc_start: 0.9586 (t80) cc_final: 0.9373 (t80) REVERT: A 552 ASP cc_start: 0.6643 (t0) cc_final: 0.5398 (m-30) REVERT: A 553 TYR cc_start: 0.8109 (p90) cc_final: 0.7586 (p90) REVERT: A 795 TYR cc_start: 0.8765 (m-10) cc_final: 0.8283 (m-10) REVERT: A 825 MET cc_start: 0.5856 (mtt) cc_final: 0.4928 (mtt) REVERT: A 967 ASP cc_start: 0.9329 (m-30) cc_final: 0.9120 (m-30) REVERT: A 1024 PHE cc_start: 0.9377 (m-10) cc_final: 0.9142 (m-80) REVERT: A 1238 GLU cc_start: 0.8181 (pt0) cc_final: 0.7961 (pt0) REVERT: A 1281 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8701 (mt-10) REVERT: A 1335 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7803 (mtm180) REVERT: A 1356 LEU cc_start: 0.8929 (tt) cc_final: 0.8705 (tt) REVERT: A 1358 ARG cc_start: 0.7921 (mpp80) cc_final: 0.7508 (mpp80) REVERT: A 1368 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8670 (tp30) REVERT: A 1371 MET cc_start: 0.8988 (mtm) cc_final: 0.8667 (mtm) REVERT: A 1389 ILE cc_start: 0.8264 (mt) cc_final: 0.7936 (mt) REVERT: C 432 ASN cc_start: 0.9576 (m-40) cc_final: 0.9089 (m110) REVERT: C 456 ASP cc_start: 0.9086 (t0) cc_final: 0.8758 (t0) REVERT: C 463 VAL cc_start: 0.9454 (t) cc_final: 0.9240 (t) REVERT: C 473 GLN cc_start: 0.8870 (mp10) cc_final: 0.8635 (mp10) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2717 time to fit residues: 102.5332 Evaluate side-chains 207 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 9.9990 chunk 93 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 887 GLN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.3588 r_free = 0.3588 target = 0.081477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.068134 restraints weight = 45914.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070261 restraints weight = 30192.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071835 restraints weight = 21785.089| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10728 Z= 0.157 Angle : 0.815 12.383 14513 Z= 0.410 Chirality : 0.048 0.264 1630 Planarity : 0.005 0.057 1865 Dihedral : 9.747 71.662 1446 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.94 % Favored : 88.60 % Rotamer: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.02 % 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: -3.31 (0.21), residues: 1307 helix: -1.32 (0.21), residues: 517 sheet: -3.16 (0.45), residues: 103 loop : -2.80 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 487 HIS 0.013 0.002 HIS A 582 PHE 0.022 0.002 PHE A1035 TYR 0.053 0.002 TYR A 950 ARG 0.011 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 314) hydrogen bonds : angle 6.53819 ( 861) covalent geometry : bond 0.00348 (10727) covalent geometry : angle 0.81521 (14513) Misc. bond : bond 0.00002 ( 1) *********************** 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 289 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 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: A 20 LEU cc_start: 0.9129 (tp) cc_final: 0.8658 (tt) REVERT: A 44 LYS cc_start: 0.9008 (mttt) cc_final: 0.8666 (mmmt) REVERT: A 68 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 77 THR cc_start: 0.9438 (m) cc_final: 0.9217 (p) REVERT: A 96 GLN cc_start: 0.8545 (tt0) cc_final: 0.8076 (tp-100) REVERT: A 97 CYS cc_start: 0.5792 (m) cc_final: 0.5332 (m) REVERT: A 216 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8206 (mm-30) REVERT: A 239 TYR cc_start: 0.8418 (m-80) cc_final: 0.8008 (m-80) REVERT: A 418 HIS cc_start: 0.8459 (m90) cc_final: 0.8188 (m-70) REVERT: A 437 ASP cc_start: 0.8212 (m-30) cc_final: 0.7988 (m-30) REVERT: A 476 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8705 (mtmm) REVERT: A 479 PHE cc_start: 0.9593 (t80) cc_final: 0.9344 (t80) REVERT: A 537 SER cc_start: 0.9309 (m) cc_final: 0.9028 (p) REVERT: A 550 LEU cc_start: 0.8408 (mp) cc_final: 0.8111 (mp) REVERT: A 552 ASP cc_start: 0.6285 (t0) cc_final: 0.5049 (m-30) REVERT: A 628 TYR cc_start: 0.8976 (m-10) cc_final: 0.8717 (m-10) REVERT: A 768 ASP cc_start: 0.9066 (t0) cc_final: 0.8771 (t0) REVERT: A 825 MET cc_start: 0.6330 (mtt) cc_final: 0.5200 (mtt) REVERT: A 941 LEU cc_start: 0.9178 (pt) cc_final: 0.8649 (pp) REVERT: A 1024 PHE cc_start: 0.9406 (m-10) cc_final: 0.9132 (m-80) REVERT: A 1102 LEU cc_start: 0.9224 (mt) cc_final: 0.9004 (mt) REVERT: A 1114 LYS cc_start: 0.8951 (mttt) cc_final: 0.8413 (tttt) REVERT: A 1276 ASP cc_start: 0.8889 (t0) cc_final: 0.8641 (t70) REVERT: A 1368 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8498 (tp30) REVERT: A 1389 ILE cc_start: 0.8271 (mt) cc_final: 0.7958 (mt) REVERT: C 432 ASN cc_start: 0.9601 (m-40) cc_final: 0.9041 (m110) REVERT: C 463 VAL cc_start: 0.9454 (t) cc_final: 0.9163 (t) REVERT: C 473 GLN cc_start: 0.8846 (mp10) cc_final: 0.8558 (mp10) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.2908 time to fit residues: 114.6208 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 : 1.254 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 74 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- 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** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN A1375 ASN C 474 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066942 restraints weight = 46343.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069027 restraints weight = 30467.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070514 restraints weight = 22103.699| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10728 Z= 0.157 Angle : 0.786 11.862 14513 Z= 0.394 Chirality : 0.046 0.252 1630 Planarity : 0.005 0.055 1865 Dihedral : 9.444 70.737 1446 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.79 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -3.12 (0.21), residues: 1307 helix: -1.11 (0.21), residues: 527 sheet: -3.22 (0.48), residues: 88 loop : -2.75 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.006 0.001 HIS A 799 PHE 0.023 0.002 PHE A 954 TYR 0.041 0.002 TYR A 950 ARG 0.008 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 314) hydrogen bonds : angle 6.36209 ( 861) covalent geometry : bond 0.00351 (10727) covalent geometry : angle 0.78649 (14513) Misc. bond : bond 0.00010 ( 1) *********************** 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 278 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.435 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 49 MET cc_start: 0.8531 (mpp) cc_final: 0.8263 (mpp) REVERT: A 63 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7282 (mtt-85) REVERT: A 68 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 77 THR cc_start: 0.9453 (m) cc_final: 0.9217 (p) REVERT: A 96 GLN cc_start: 0.8616 (tt0) cc_final: 0.7957 (tp-100) REVERT: A 418 HIS cc_start: 0.8474 (m90) cc_final: 0.8137 (m-70) REVERT: A 476 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8702 (mtmm) REVERT: A 479 PHE cc_start: 0.9559 (t80) cc_final: 0.9317 (t80) REVERT: A 550 LEU cc_start: 0.8495 (mp) cc_final: 0.8123 (mp) REVERT: A 552 ASP cc_start: 0.6416 (t0) cc_final: 0.4998 (m-30) REVERT: A 628 TYR cc_start: 0.8983 (m-10) cc_final: 0.8665 (m-10) REVERT: A 635 LEU cc_start: 0.8621 (pp) cc_final: 0.8222 (pp) REVERT: A 825 MET cc_start: 0.6612 (mtt) cc_final: 0.5367 (mtt) REVERT: A 830 ASP cc_start: 0.8933 (p0) cc_final: 0.8707 (p0) REVERT: A 941 LEU cc_start: 0.9235 (pt) cc_final: 0.8687 (pp) REVERT: A 1024 PHE cc_start: 0.9402 (m-10) cc_final: 0.9054 (m-80) REVERT: A 1102 LEU cc_start: 0.9217 (mt) cc_final: 0.9014 (mt) REVERT: A 1114 LYS cc_start: 0.9019 (mttt) cc_final: 0.8457 (tttt) REVERT: A 1209 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9082 (mtmm) REVERT: A 1238 GLU cc_start: 0.8116 (pt0) cc_final: 0.7685 (pt0) REVERT: A 1371 MET cc_start: 0.9278 (ptp) cc_final: 0.8906 (ptp) REVERT: A 1389 ILE cc_start: 0.8258 (mt) cc_final: 0.7952 (mt) REVERT: C 432 ASN cc_start: 0.9561 (m-40) cc_final: 0.9089 (m110) REVERT: C 455 GLU cc_start: 0.8841 (mp0) cc_final: 0.8419 (mp0) REVERT: C 456 ASP cc_start: 0.8874 (t0) cc_final: 0.8529 (t0) REVERT: C 463 VAL cc_start: 0.9454 (t) cc_final: 0.9183 (t) REVERT: C 473 GLN cc_start: 0.8903 (mp10) cc_final: 0.8581 (mp10) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3619 time to fit residues: 137.2796 Evaluate side-chains 210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** 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 ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3631 r_free = 0.3631 target = 0.083619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070108 restraints weight = 45734.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072341 restraints weight = 29534.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073946 restraints weight = 21097.910| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10728 Z= 0.154 Angle : 0.819 11.243 14513 Z= 0.404 Chirality : 0.047 0.247 1630 Planarity : 0.006 0.124 1865 Dihedral : 9.256 67.419 1446 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.86 % Favored : 88.60 % 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 : 0.00 % 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: -3.00 (0.22), residues: 1307 helix: -0.96 (0.22), residues: 520 sheet: -3.42 (0.38), residues: 124 loop : -2.59 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 220 HIS 0.007 0.001 HIS A 544 PHE 0.027 0.001 PHE A1035 TYR 0.050 0.002 TYR A 87 ARG 0.032 0.001 ARG A 915 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 314) hydrogen bonds : angle 6.22033 ( 861) covalent geometry : bond 0.00345 (10727) covalent geometry : angle 0.81925 (14513) Misc. bond : bond 0.00006 ( 1) *********************** 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 279 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.141 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 43 HIS cc_start: 0.9286 (m90) cc_final: 0.9047 (m-70) REVERT: A 49 MET cc_start: 0.8598 (mpp) cc_final: 0.8206 (mpp) REVERT: A 96 GLN cc_start: 0.8154 (tt0) cc_final: 0.7943 (tp40) REVERT: A 115 GLU cc_start: 0.9156 (tt0) cc_final: 0.8932 (tt0) REVERT: A 418 HIS cc_start: 0.8587 (m90) cc_final: 0.8227 (m-70) REVERT: A 444 HIS cc_start: 0.8080 (t70) cc_final: 0.7790 (t-90) REVERT: A 476 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8659 (mtmm) REVERT: A 552 ASP cc_start: 0.6450 (t0) cc_final: 0.4928 (m-30) REVERT: A 628 TYR cc_start: 0.8962 (m-10) cc_final: 0.8743 (m-10) REVERT: A 635 LEU cc_start: 0.8457 (pp) cc_final: 0.7905 (pp) REVERT: A 825 MET cc_start: 0.6527 (mtt) cc_final: 0.5398 (mtt) REVERT: A 830 ASP cc_start: 0.8934 (p0) cc_final: 0.8703 (p0) REVERT: A 941 LEU cc_start: 0.9174 (pt) cc_final: 0.8556 (pp) REVERT: A 1024 PHE cc_start: 0.9403 (m-10) cc_final: 0.8988 (m-80) REVERT: A 1114 LYS cc_start: 0.8993 (mttt) cc_final: 0.8635 (tttt) REVERT: C 432 ASN cc_start: 0.9471 (m-40) cc_final: 0.9024 (m110) REVERT: C 455 GLU cc_start: 0.8768 (mp0) cc_final: 0.8372 (mp0) REVERT: C 456 ASP cc_start: 0.8776 (t0) cc_final: 0.8461 (t0) REVERT: C 463 VAL cc_start: 0.9454 (t) cc_final: 0.9182 (t) REVERT: C 473 GLN cc_start: 0.8816 (mp10) cc_final: 0.8500 (mp10) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3200 time to fit residues: 122.2280 Evaluate side-chains 214 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 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 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 = 0.3607 r_free = 0.3607 target = 0.081977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068387 restraints weight = 46465.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070629 restraints weight = 29953.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072228 restraints weight = 21403.023| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10728 Z= 0.162 Angle : 0.808 11.322 14513 Z= 0.401 Chirality : 0.048 0.237 1630 Planarity : 0.005 0.053 1865 Dihedral : 9.078 65.203 1446 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.25 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -2.79 (0.22), residues: 1307 helix: -0.73 (0.22), residues: 506 sheet: -3.40 (0.45), residues: 95 loop : -2.55 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.006 0.001 HIS A 799 PHE 0.043 0.002 PHE A 954 TYR 0.049 0.002 TYR A 950 ARG 0.014 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 314) hydrogen bonds : angle 6.16704 ( 861) covalent geometry : bond 0.00364 (10727) covalent geometry : angle 0.80797 (14513) Misc. bond : bond 0.00031 ( 1) *********************** 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 262 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.309 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 49 MET cc_start: 0.8653 (mpp) cc_final: 0.8233 (mpp) REVERT: A 62 LYS cc_start: 0.9362 (mppt) cc_final: 0.9043 (mppt) REVERT: A 68 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 96 GLN cc_start: 0.8326 (tt0) cc_final: 0.8030 (tp40) REVERT: A 97 CYS cc_start: 0.6494 (m) cc_final: 0.6209 (m) REVERT: A 115 GLU cc_start: 0.9163 (tt0) cc_final: 0.8938 (tt0) REVERT: A 216 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8720 (mm-30) REVERT: A 418 HIS cc_start: 0.8598 (m90) cc_final: 0.8274 (m-70) REVERT: A 450 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8878 (tp-100) REVERT: A 476 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8632 (mtmm) REVERT: A 597 LEU cc_start: 0.8961 (tt) cc_final: 0.8723 (tt) REVERT: A 628 TYR cc_start: 0.8937 (m-10) cc_final: 0.8650 (m-10) REVERT: A 635 LEU cc_start: 0.8423 (pp) cc_final: 0.7874 (pp) REVERT: A 825 MET cc_start: 0.6633 (mtt) cc_final: 0.5480 (mtt) REVERT: A 862 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 905 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.8663 (ttm-80) REVERT: A 941 LEU cc_start: 0.9243 (pt) cc_final: 0.8629 (pp) REVERT: A 1024 PHE cc_start: 0.9404 (m-10) cc_final: 0.9021 (m-80) REVERT: A 1114 LYS cc_start: 0.9024 (mttt) cc_final: 0.8663 (tttt) REVERT: A 1294 LEU cc_start: 0.8839 (mt) cc_final: 0.8618 (mt) REVERT: A 1389 ILE cc_start: 0.7951 (mt) cc_final: 0.7658 (mt) REVERT: C 432 ASN cc_start: 0.9439 (m-40) cc_final: 0.9002 (m110) REVERT: C 455 GLU cc_start: 0.8785 (mp0) cc_final: 0.8383 (mp0) REVERT: C 456 ASP cc_start: 0.8775 (t0) cc_final: 0.8426 (t0) REVERT: C 463 VAL cc_start: 0.9453 (t) cc_final: 0.9162 (t) REVERT: C 466 MET cc_start: 0.9013 (ppp) cc_final: 0.8792 (ppp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2593 time to fit residues: 93.1977 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 : 1.161 ------------------------------------------------------------------------------- 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: 4.9990 chunk 121 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 4 optimal weight: 0.0570 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 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 C 441 GLN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3639 r_free = 0.3639 target = 0.083930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070156 restraints weight = 45358.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072442 restraints weight = 29395.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074083 restraints weight = 20955.703| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10728 Z= 0.138 Angle : 0.790 10.893 14513 Z= 0.389 Chirality : 0.047 0.220 1630 Planarity : 0.005 0.054 1865 Dihedral : 8.899 67.397 1446 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.02 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.68 (0.22), residues: 1307 helix: -0.59 (0.23), residues: 507 sheet: -3.66 (0.44), residues: 96 loop : -2.48 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.005 0.001 HIS A 799 PHE 0.021 0.001 PHE A1035 TYR 0.033 0.002 TYR A 950 ARG 0.008 0.001 ARG A1184 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 314) hydrogen bonds : angle 5.94319 ( 861) covalent geometry : bond 0.00307 (10727) covalent geometry : angle 0.79026 (14513) Misc. bond : bond 0.00013 ( 1) *********************** 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 269 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.465 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: A 49 MET cc_start: 0.8662 (mpp) cc_final: 0.8226 (mpp) REVERT: A 62 LYS cc_start: 0.9309 (mppt) cc_final: 0.8974 (mppt) REVERT: A 96 GLN cc_start: 0.8252 (tt0) cc_final: 0.7837 (tp40) REVERT: A 115 GLU cc_start: 0.9166 (tt0) cc_final: 0.8912 (tt0) REVERT: A 216 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 418 HIS cc_start: 0.8507 (m90) cc_final: 0.8152 (m-70) REVERT: A 476 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8552 (mtmm) REVERT: A 597 LEU cc_start: 0.8968 (tt) cc_final: 0.8472 (tt) REVERT: A 600 GLN cc_start: 0.8335 (pp30) cc_final: 0.8067 (pm20) REVERT: A 628 TYR cc_start: 0.8971 (m-10) cc_final: 0.8652 (m-10) REVERT: A 635 LEU cc_start: 0.8433 (pp) cc_final: 0.7800 (pp) REVERT: A 825 MET cc_start: 0.5917 (mtt) cc_final: 0.5635 (mtt) REVERT: A 941 LEU cc_start: 0.9157 (pt) cc_final: 0.8470 (pp) REVERT: A 1024 PHE cc_start: 0.9423 (m-10) cc_final: 0.9006 (m-80) REVERT: A 1042 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8460 (mm-30) REVERT: A 1114 LYS cc_start: 0.8971 (mttt) cc_final: 0.8664 (tttt) REVERT: A 1123 ARG cc_start: 0.8207 (mtt180) cc_final: 0.6715 (ptp-170) REVERT: A 1196 MET cc_start: 0.8684 (ptp) cc_final: 0.8086 (mpp) REVERT: A 1281 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 1294 LEU cc_start: 0.8849 (mt) cc_final: 0.8610 (mt) REVERT: C 435 LYS cc_start: 0.9324 (tmtt) cc_final: 0.9076 (tmtt) REVERT: C 455 GLU cc_start: 0.8865 (mp0) cc_final: 0.8493 (mp0) REVERT: C 463 VAL cc_start: 0.9459 (t) cc_final: 0.9147 (t) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2659 time to fit residues: 97.4199 Evaluate side-chains 214 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 8.9990 chunk 81 optimal weight: 0.0670 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 79 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 0.7730 ------------------------------------------------------------------------------- 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 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.084814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070968 restraints weight = 45729.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073257 restraints weight = 29592.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074922 restraints weight = 21106.381| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10728 Z= 0.146 Angle : 0.800 10.620 14513 Z= 0.394 Chirality : 0.047 0.217 1630 Planarity : 0.005 0.080 1865 Dihedral : 8.764 69.283 1446 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.25 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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 (0.22), residues: 1307 helix: -0.49 (0.23), residues: 510 sheet: -3.67 (0.41), residues: 107 loop : -2.42 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.005 0.001 HIS A 799 PHE 0.047 0.002 PHE A 954 TYR 0.033 0.002 TYR A 950 ARG 0.014 0.001 ARG A1380 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 314) hydrogen bonds : angle 6.01796 ( 861) covalent geometry : bond 0.00323 (10727) covalent geometry : angle 0.80010 (14513) Misc. bond : bond 0.00028 ( 1) *********************** 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 261 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.107 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 49 MET cc_start: 0.8634 (mpp) cc_final: 0.8364 (mpp) REVERT: A 62 LYS cc_start: 0.9283 (mppt) cc_final: 0.8993 (mppt) REVERT: A 68 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 96 GLN cc_start: 0.8248 (tt0) cc_final: 0.7853 (tp40) REVERT: A 115 GLU cc_start: 0.9153 (tt0) cc_final: 0.8894 (tt0) REVERT: A 216 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 418 HIS cc_start: 0.8446 (m90) cc_final: 0.8097 (m-70) REVERT: A 476 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8507 (mtmm) REVERT: A 628 TYR cc_start: 0.8940 (m-10) cc_final: 0.8689 (m-10) REVERT: A 635 LEU cc_start: 0.8400 (pp) cc_final: 0.7842 (pp) REVERT: A 729 MET cc_start: 0.8840 (mmp) cc_final: 0.8278 (mmp) REVERT: A 941 LEU cc_start: 0.9292 (pt) cc_final: 0.8673 (pp) REVERT: A 1021 MET cc_start: 0.9399 (ptp) cc_final: 0.9163 (ptt) REVERT: A 1024 PHE cc_start: 0.9432 (m-10) cc_final: 0.9030 (m-80) REVERT: A 1114 LYS cc_start: 0.8976 (mttt) cc_final: 0.8649 (tttt) REVERT: A 1123 ARG cc_start: 0.8142 (mtt180) cc_final: 0.6447 (ptp90) REVERT: A 1281 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 1294 LEU cc_start: 0.8871 (mt) cc_final: 0.8618 (mt) REVERT: A 1311 ARG cc_start: 0.8894 (ptp90) cc_final: 0.8423 (mtt180) REVERT: A 1389 ILE cc_start: 0.7574 (mt) cc_final: 0.6998 (mt) REVERT: C 435 LYS cc_start: 0.9333 (tmtt) cc_final: 0.9109 (tmtt) REVERT: C 437 ASP cc_start: 0.8889 (m-30) cc_final: 0.8616 (m-30) REVERT: C 443 ILE cc_start: 0.8948 (mm) cc_final: 0.8637 (mt) REVERT: C 455 GLU cc_start: 0.8910 (mp0) cc_final: 0.8511 (mp0) REVERT: C 456 ASP cc_start: 0.8722 (t0) cc_final: 0.8435 (t0) REVERT: C 463 VAL cc_start: 0.9426 (t) cc_final: 0.9085 (t) REVERT: C 466 MET cc_start: 0.8974 (ppp) cc_final: 0.8739 (ppp) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2703 time to fit residues: 96.6241 Evaluate side-chains 207 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 206 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A1008 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 ** A1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3640 r_free = 0.3640 target = 0.083723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069952 restraints weight = 45422.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072215 restraints weight = 29572.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073823 restraints weight = 21155.774| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10728 Z= 0.151 Angle : 0.803 11.843 14513 Z= 0.396 Chirality : 0.047 0.240 1630 Planarity : 0.005 0.064 1865 Dihedral : 8.775 70.104 1446 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.40 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -2.57 (0.22), residues: 1307 helix: -0.46 (0.23), residues: 518 sheet: -3.68 (0.40), residues: 107 loop : -2.42 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS A 799 PHE 0.024 0.002 PHE A1314 TYR 0.022 0.001 TYR A 950 ARG 0.015 0.001 ARG A1380 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 314) hydrogen bonds : angle 5.85040 ( 861) covalent geometry : bond 0.00342 (10727) covalent geometry : angle 0.80327 (14513) Misc. bond : bond 0.00028 ( 1) ********************** 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 260 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.276 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: A 43 HIS cc_start: 0.9035 (m90) cc_final: 0.8804 (m90) REVERT: A 49 MET cc_start: 0.8503 (mpp) cc_final: 0.8246 (mpp) REVERT: A 62 LYS cc_start: 0.9309 (mppt) cc_final: 0.8987 (mppt) REVERT: A 64 LEU cc_start: 0.9299 (mm) cc_final: 0.9098 (mm) REVERT: A 68 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 96 GLN cc_start: 0.8352 (tt0) cc_final: 0.7955 (tp40) REVERT: A 115 GLU cc_start: 0.9202 (tt0) cc_final: 0.8926 (tt0) REVERT: A 216 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8771 (mm-30) REVERT: A 407 LEU cc_start: 0.9282 (tp) cc_final: 0.8716 (tp) REVERT: A 418 HIS cc_start: 0.8482 (m90) cc_final: 0.8103 (m-70) REVERT: A 476 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8573 (mtmm) REVERT: A 628 TYR cc_start: 0.8949 (m-10) cc_final: 0.8644 (m-10) REVERT: A 635 LEU cc_start: 0.8461 (pp) cc_final: 0.7834 (pp) REVERT: A 825 MET cc_start: 0.6080 (mtt) cc_final: 0.4901 (ttm) REVERT: A 941 LEU cc_start: 0.9280 (pt) cc_final: 0.8628 (pp) REVERT: A 1021 MET cc_start: 0.9417 (ptp) cc_final: 0.9170 (ptt) REVERT: A 1024 PHE cc_start: 0.9429 (m-10) cc_final: 0.9025 (m-80) REVERT: A 1114 LYS cc_start: 0.9015 (mttt) cc_final: 0.8664 (tttt) REVERT: A 1123 ARG cc_start: 0.7925 (mtt180) cc_final: 0.6444 (ptp90) REVERT: A 1196 MET cc_start: 0.8609 (ptp) cc_final: 0.8234 (mpp) REVERT: A 1277 ASP cc_start: 0.8676 (t70) cc_final: 0.8146 (t0) REVERT: A 1281 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 1294 LEU cc_start: 0.8935 (mt) cc_final: 0.8734 (mt) REVERT: A 1339 GLN cc_start: 0.8094 (mm110) cc_final: 0.7591 (mm110) REVERT: A 1380 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7898 (ttp80) REVERT: C 435 LYS cc_start: 0.9334 (tmtt) cc_final: 0.9121 (tmtt) REVERT: C 437 ASP cc_start: 0.8929 (m-30) cc_final: 0.8619 (m-30) REVERT: C 455 GLU cc_start: 0.8884 (mp0) cc_final: 0.8650 (mp0) REVERT: C 456 ASP cc_start: 0.8715 (t0) cc_final: 0.8463 (t0) REVERT: C 463 VAL cc_start: 0.9442 (t) cc_final: 0.9110 (t) REVERT: C 466 MET cc_start: 0.8983 (ppp) cc_final: 0.8763 (ppp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2872 time to fit residues: 102.3181 Evaluate side-chains 201 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 463 ASN A 544 HIS ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 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 ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3669 r_free = 0.3669 target = 0.085705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071759 restraints weight = 44109.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074036 restraints weight = 28900.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075661 restraints weight = 20811.505| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10728 Z= 0.141 Angle : 0.815 12.209 14513 Z= 0.400 Chirality : 0.047 0.256 1630 Planarity : 0.005 0.059 1865 Dihedral : 8.637 74.116 1446 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.02 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.49 (0.23), residues: 1307 helix: -0.39 (0.23), residues: 512 sheet: -3.49 (0.42), residues: 102 loop : -2.40 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 76 HIS 0.008 0.001 HIS A1249 PHE 0.033 0.001 PHE A 954 TYR 0.029 0.002 TYR A 950 ARG 0.013 0.001 ARG A1380 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 314) hydrogen bonds : angle 5.78170 ( 861) covalent geometry : bond 0.00315 (10727) covalent geometry : angle 0.81542 (14513) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.80 seconds wall clock time: 75 minutes 37.79 seconds (4537.79 seconds total)