Starting phenix.real_space_refine on Mon Jun 23 20:47:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmd_34896/06_2025/8hmd_34896.cif" } resolution = 4.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 152 5.16 5 C 17396 2.51 5 N 4607 2.21 5 O 5215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27372 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5686 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 17, 'TRANS': 694} Chain: "B" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9690 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 39, 'TRANS': 1155} Chain: "C" Number of atoms: 10821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10821 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 34, 'TRANS': 1299} Chain: "F" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14704 SG CYS B1111 64.275 138.027 137.566 1.00297.89 S ATOM 15022 SG CYS B1152 72.471 114.322 144.203 1.00277.14 S ATOM 15045 SG CYS B1155 71.106 114.984 140.726 1.00299.44 S ATOM 15190 SG CYS B1172 68.738 113.818 143.413 1.00263.60 S ATOM 15209 SG CYS B1175 71.368 111.402 142.118 1.00253.29 S Time building chain proxies: 14.05, per 1000 atoms: 0.51 Number of scatterers: 27372 At special positions: 0 Unit cell: (173.8, 195.8, 216.7, 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) Zn 2 29.99 S 152 16.00 O 5215 8.00 N 4607 7.00 C 17396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 857 " - pdb=" SG CYS B 876 " distance=2.04 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 367 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.21 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1175 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1155 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1152 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1172 " Number of angles added : 6 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 29 sheets defined 52.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 582 through 593 removed outlier: 3.587A pdb=" N ARG A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.832A pdb=" N ILE A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 4.352A pdb=" N LYS A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.998A pdb=" N TYR A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 4.048A pdb=" N SER A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.128A pdb=" N ILE A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.116A pdb=" N THR A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.688A pdb=" N MET B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS B 680 " --> pdb=" O VAL B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 699 through 710 Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'B' and resid 728 through 739 removed outlier: 4.002A pdb=" N ASN B 739 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 752 Processing helix chain 'B' and resid 753 through 765 removed outlier: 4.097A pdb=" N SER B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 775 removed outlier: 3.875A pdb=" N VAL B 770 " --> pdb=" O ASP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 798 removed outlier: 3.919A pdb=" N LEU B 784 " --> pdb=" O GLN B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 Processing helix chain 'B' and resid 813 through 825 Processing helix chain 'B' and resid 826 through 837 removed outlier: 3.858A pdb=" N LEU B 830 " --> pdb=" O ASP B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 855 removed outlier: 3.776A pdb=" N GLN B 845 " --> pdb=" O ASN B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 Processing helix chain 'B' and resid 870 through 880 Processing helix chain 'B' and resid 882 through 894 Processing helix chain 'B' and resid 896 through 912 removed outlier: 4.492A pdb=" N GLY B 900 " --> pdb=" O VAL B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 925 Processing helix chain 'B' and resid 927 through 944 removed outlier: 3.515A pdb=" N ALA B 931 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 976 removed outlier: 3.672A pdb=" N ILE B 952 " --> pdb=" O ASN B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 995 removed outlier: 3.523A pdb=" N ASN B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1005 Processing helix chain 'B' and resid 1007 through 1025 Processing helix chain 'B' and resid 1027 through 1042 Processing helix chain 'B' and resid 1046 through 1062 removed outlier: 3.580A pdb=" N ILE B1050 " --> pdb=" O ASP B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.685A pdb=" N CYS B1067 " --> pdb=" O SER B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1099 removed outlier: 3.948A pdb=" N HIS B1099 " --> pdb=" O ILE B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1168 Processing helix chain 'B' and resid 1180 through 1195 removed outlier: 3.519A pdb=" N PHE B1184 " --> pdb=" O ASP B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Processing helix chain 'C' and resid 26 through 42 Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.955A pdb=" N ILE C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.736A pdb=" N SER C 69 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 95 through 113 removed outlier: 4.496A pdb=" N ARG C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 145 through 160 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.819A pdb=" N GLN C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 219 through 232 removed outlier: 3.571A pdb=" N ILE C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 249 Processing helix chain 'C' and resid 252 through 266 Processing helix chain 'C' and resid 269 through 288 Processing helix chain 'C' and resid 291 through 305 removed outlier: 3.506A pdb=" N ILE C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 327 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.906A pdb=" N PHE C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.612A pdb=" N LEU C 368 " --> pdb=" O ASN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 401 through 415 Processing helix chain 'C' and resid 419 through 440 removed outlier: 3.957A pdb=" N THR C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.944A pdb=" N GLN C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 Processing helix chain 'C' and resid 481 through 497 Processing helix chain 'C' and resid 500 through 514 Processing helix chain 'C' and resid 516 through 531 Processing helix chain 'C' and resid 534 through 548 Processing helix chain 'C' and resid 550 through 565 removed outlier: 3.703A pdb=" N ASN C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 570 Processing helix chain 'C' and resid 571 through 585 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 605 through 612 Processing helix chain 'C' and resid 623 through 641 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 661 through 678 removed outlier: 4.368A pdb=" N VAL C 665 " --> pdb=" O THR C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 690 removed outlier: 3.749A pdb=" N ALA C 684 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 713 removed outlier: 3.539A pdb=" N ASP C 711 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 730 removed outlier: 4.159A pdb=" N TYR C 723 " --> pdb=" O TYR C 719 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU C 726 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 747 Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 766 through 780 Processing helix chain 'C' and resid 782 through 797 removed outlier: 3.531A pdb=" N ALA C 786 " --> pdb=" O ASP C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 814 Processing helix chain 'C' and resid 816 through 831 Proline residue: C 826 - end of helix Processing helix chain 'C' and resid 837 through 858 Processing helix chain 'C' and resid 867 through 891 Processing helix chain 'C' and resid 895 through 917 removed outlier: 3.820A pdb=" N TYR C 916 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 917 " --> pdb=" O THR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 934 Processing helix chain 'C' and resid 944 through 962 Processing helix chain 'C' and resid 963 through 978 removed outlier: 3.751A pdb=" N CYS C 967 " --> pdb=" O GLN C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 1000 through 1012 Processing helix chain 'C' and resid 1015 through 1029 Processing helix chain 'C' and resid 1031 through 1045 removed outlier: 3.678A pdb=" N ALA C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1065 Processing helix chain 'C' and resid 1067 through 1079 removed outlier: 3.728A pdb=" N ALA C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1098 Processing helix chain 'C' and resid 1117 through 1131 Processing helix chain 'C' and resid 1136 through 1150 Processing helix chain 'C' and resid 1151 through 1154 removed outlier: 4.226A pdb=" N TYR C1154 " --> pdb=" O GLY C1151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1151 through 1154' Processing helix chain 'C' and resid 1156 through 1172 Processing helix chain 'C' and resid 1175 through 1189 removed outlier: 3.617A pdb=" N MET C1179 " --> pdb=" O TYR C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1204 Processing helix chain 'C' and resid 1211 through 1228 removed outlier: 3.503A pdb=" N LEU C1215 " --> pdb=" O TYR C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1246 removed outlier: 3.716A pdb=" N ALA C1235 " --> pdb=" O LYS C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1250 through 1263 Processing helix chain 'C' and resid 1265 through 1280 Processing helix chain 'C' and resid 1285 through 1298 Processing helix chain 'C' and resid 1300 through 1315 Processing helix chain 'C' and resid 1318 through 1323 removed outlier: 4.447A pdb=" N GLU C1322 " --> pdb=" O TYR C1318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1318 through 1323' Processing helix chain 'C' and resid 1325 through 1334 removed outlier: 4.543A pdb=" N LYS C1334 " --> pdb=" O ARG C1330 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 37 through 40 removed outlier: 4.230A pdb=" N LEU F 40 " --> pdb=" O ASN F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.509A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 3.692A pdb=" N ILE F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.757A pdb=" N GLU F 89 " --> pdb=" O PRO F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.950A pdb=" N ILE F 99 " --> pdb=" O LEU F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 131 Processing helix chain 'F' and resid 132 through 139 Processing helix chain 'F' and resid 141 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.980A pdb=" N MET A 313 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR A 8 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 311 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 7.056A pdb=" N ALA A 82 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 70 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 80 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER A 92 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.706A pdb=" N ASP A 132 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.931A pdb=" N GLY A 167 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS A 155 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 165 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 197 removed outlier: 4.096A pdb=" N CYS A 194 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 238 through 243 removed outlier: 6.988A pdb=" N SER A 253 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 241 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 251 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE A 243 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 249 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 254 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 259 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 270 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR A 263 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE A 268 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 363 removed outlier: 4.099A pdb=" N ASN A 359 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 377 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A 393 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY A 379 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 391 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.657A pdb=" N ILE A 403 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 419 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 431 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 421 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 438 through 443 removed outlier: 3.761A pdb=" N CYS A 440 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 462 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 484 through 487 removed outlier: 3.938A pdb=" N ASN A 484 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 515 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP A 507 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN A 513 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 522 through 525 Processing sheet with id=AB5, first strand: chain 'A' and resid 558 through 563 removed outlier: 5.864A pdb=" N VAL A 559 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 570 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 561 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 9 removed outlier: 5.313A pdb=" N PHE B 334 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS B 8 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 332 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B 314 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.584A pdb=" N ALA B 19 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 40 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 64 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 73 through 78 removed outlier: 4.353A pdb=" N LEU B 75 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL B 96 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 98 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B 107 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 100 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B 105 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 161 through 164 removed outlier: 7.101A pdb=" N VAL B 180 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 192 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 182 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 214 through 219 removed outlier: 3.902A pdb=" N TYR B 238 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 261 through 268 removed outlier: 3.763A pdb=" N THR B 280 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER B 278 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL B 266 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 276 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP B 268 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET B 274 " --> pdb=" O TRP B 268 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 302 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 343 through 345 Processing sheet with id=AC5, first strand: chain 'B' and resid 385 through 388 removed outlier: 3.692A pdb=" N LEU B 404 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU B 409 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP B 418 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AC7, first strand: chain 'B' and resid 501 through 506 removed outlier: 4.607A pdb=" N THR B 503 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 522 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN B 532 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 524 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU B 530 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 545 removed outlier: 4.030A pdb=" N ILE B 563 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 572 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.634A pdb=" N ASN B 606 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 583 through 586 removed outlier: 3.501A pdb=" N ILE B 614 " --> pdb=" O MET B 602 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 619 through 624 removed outlier: 6.690A pdb=" N LYS B 629 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 623 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) 1506 hydrogen bonds defined for protein. 4377 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: 12.73 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8946 1.34 - 1.46: 6140 1.46 - 1.59: 12559 1.59 - 1.71: 0 1.71 - 1.84: 234 Bond restraints: 27879 Sorted by residual: bond pdb=" CG MET C 651 " pdb=" SD MET C 651 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.30e+00 bond pdb=" CB MET C 651 " pdb=" CG MET C 651 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" SD MET C1092 " pdb=" CE MET C1092 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CD GLU C 728 " pdb=" OE1 GLU C 728 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.62e+00 bond pdb=" CG GLU C 728 " pdb=" CD GLU C 728 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 27874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 37357 2.82 - 5.65: 223 5.65 - 8.47: 36 8.47 - 11.30: 2 11.30 - 14.12: 2 Bond angle restraints: 37620 Sorted by residual: angle pdb=" C ASP C1116 " pdb=" CA ASP C1116 " pdb=" CB ASP C1116 " ideal model delta sigma weight residual 115.79 109.91 5.88 1.19e+00 7.06e-01 2.45e+01 angle pdb=" N ILE B1125 " pdb=" CA ILE B1125 " pdb=" C ILE B1125 " ideal model delta sigma weight residual 113.47 108.69 4.78 1.01e+00 9.80e-01 2.24e+01 angle pdb=" CB MET C 905 " pdb=" CG MET C 905 " pdb=" SD MET C 905 " ideal model delta sigma weight residual 112.70 98.58 14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CB MET C 651 " pdb=" CG MET C 651 " pdb=" SD MET C 651 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N ILE C1132 " pdb=" CA ILE C1132 " pdb=" C ILE C1132 " ideal model delta sigma weight residual 113.42 108.93 4.49 1.17e+00 7.31e-01 1.47e+01 ... (remaining 37615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15371 17.94 - 35.88: 1379 35.88 - 53.82: 244 53.82 - 71.76: 46 71.76 - 89.69: 22 Dihedral angle restraints: 17062 sinusoidal: 7050 harmonic: 10012 Sorted by residual: dihedral pdb=" CB CYS B 857 " pdb=" SG CYS B 857 " pdb=" SG CYS B 876 " pdb=" CB CYS B 876 " ideal model delta sinusoidal sigma weight residual 93.00 175.10 -82.10 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS C 335 " pdb=" SG CYS C 335 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual -86.00 -137.35 51.35 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" CA GLU A 696 " pdb=" C GLU A 696 " pdb=" N PHE A 697 " pdb=" CA PHE A 697 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 17059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3039 0.041 - 0.082: 803 0.082 - 0.122: 261 0.122 - 0.163: 27 0.163 - 0.204: 3 Chirality restraints: 4133 Sorted by residual: chirality pdb=" CG LEU C 739 " pdb=" CB LEU C 739 " pdb=" CD1 LEU C 739 " pdb=" CD2 LEU C 739 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA MET B 246 " pdb=" N MET B 246 " pdb=" C MET B 246 " pdb=" CB MET B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4130 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 598 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C ALA C 598 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA C 598 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR C 599 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 48 " 0.016 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE C 48 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C 48 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 48 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 48 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 48 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 48 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 164 " 0.013 2.00e-02 2.50e+03 1.39e-02 4.81e+00 pdb=" CG TRP B 164 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 164 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 164 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 164 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 164 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 164 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 164 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 164 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 164 " -0.004 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 471 2.69 - 3.25: 27091 3.25 - 3.80: 42444 3.80 - 4.35: 54709 4.35 - 4.90: 89795 Nonbonded interactions: 214510 Sorted by model distance: nonbonded pdb=" OG SER B 587 " pdb=" O ILE B 590 " model vdw 2.143 3.040 nonbonded pdb=" NE1 TRP A 691 " pdb=" OE2 GLU A 696 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASP B 663 " pdb=" NZ LYS B 667 " model vdw 2.174 3.120 nonbonded pdb=" O GLY C 510 " pdb=" OG SER C 513 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN C 278 " pdb=" NE2 GLN C 282 " model vdw 2.254 3.120 ... (remaining 214505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 66.270 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27886 Z= 0.131 Angle : 0.620 14.120 37630 Z= 0.348 Chirality : 0.041 0.204 4133 Planarity : 0.003 0.054 4858 Dihedral : 14.083 89.695 10576 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3379 helix: 1.30 (0.13), residues: 1672 sheet: 0.33 (0.22), residues: 592 loop : -1.99 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 164 HIS 0.006 0.001 HIS B1014 PHE 0.037 0.001 PHE C 48 TYR 0.023 0.001 TYR C 21 ARG 0.003 0.000 ARG C 266 Details of bonding type rmsd hydrogen bonds : bond 0.12574 ( 1498) hydrogen bonds : angle 5.29329 ( 4377) metal coordination : bond 0.00138 ( 5) metal coordination : angle 1.59373 ( 6) SS BOND : bond 0.00420 ( 2) SS BOND : angle 3.31538 ( 4) covalent geometry : bond 0.00257 (27879) covalent geometry : angle 0.61910 (37620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 2.921 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 356 LEU cc_start: 0.8911 (tp) cc_final: 0.8639 (pp) REVERT: A 513 GLN cc_start: 0.9493 (tt0) cc_final: 0.9205 (tm-30) REVERT: A 661 GLN cc_start: 0.9551 (tp-100) cc_final: 0.9287 (tp-100) REVERT: B 170 MET cc_start: 0.8657 (ppp) cc_final: 0.7787 (ppp) REVERT: B 188 MET cc_start: 0.8644 (tmm) cc_final: 0.8376 (tmm) REVERT: B 190 MET cc_start: 0.9427 (mtm) cc_final: 0.8924 (mtt) REVERT: B 246 MET cc_start: 0.8566 (mmp) cc_final: 0.8139 (mmm) REVERT: B 346 MET cc_start: 0.8454 (mtt) cc_final: 0.8221 (mtp) REVERT: B 891 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8409 (mm-30) REVERT: B 1048 LYS cc_start: 0.8814 (tttt) cc_final: 0.8445 (tptt) REVERT: C 30 MET cc_start: -0.0538 (mmp) cc_final: -0.5399 (mmt) REVERT: C 127 PHE cc_start: 0.3908 (m-80) cc_final: 0.3655 (m-10) REVERT: C 189 MET cc_start: -0.4277 (mmt) cc_final: -0.5681 (mmt) REVERT: C 396 ASN cc_start: 0.8869 (m-40) cc_final: 0.8624 (m-40) REVERT: C 595 MET cc_start: 0.4910 (mtp) cc_final: 0.4075 (mmm) REVERT: C 617 MET cc_start: -0.4112 (mmp) cc_final: -0.4783 (ptp) REVERT: C 716 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7711 (mtt180) REVERT: C 719 TYR cc_start: 0.7931 (t80) cc_final: 0.7300 (t80) REVERT: C 796 MET cc_start: 0.7121 (mpp) cc_final: 0.5957 (tmm) REVERT: C 940 MET cc_start: 0.8528 (mmp) cc_final: 0.8282 (mmp) REVERT: C 1033 ASN cc_start: 0.9429 (m-40) cc_final: 0.9175 (p0) REVERT: C 1256 MET cc_start: 0.9457 (tpt) cc_final: 0.9042 (tpp) REVERT: F 100 LEU cc_start: 0.7888 (pp) cc_final: 0.7631 (pp) REVERT: F 144 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8704 (mp0) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.4417 time to fit residues: 206.2277 Evaluate side-chains 164 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 264 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN ** B1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 ASN B1193 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 671 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.050317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.035171 restraints weight = 369579.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.035940 restraints weight = 276910.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.036457 restraints weight = 223920.401| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27886 Z= 0.162 Angle : 0.568 7.930 37630 Z= 0.308 Chirality : 0.041 0.196 4133 Planarity : 0.003 0.056 4858 Dihedral : 4.173 26.078 3656 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 0.23 % Allowed : 2.99 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3379 helix: 1.51 (0.13), residues: 1705 sheet: 0.27 (0.22), residues: 589 loop : -1.86 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 767 HIS 0.006 0.001 HIS A 392 PHE 0.020 0.001 PHE C 45 TYR 0.013 0.001 TYR B 68 ARG 0.005 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1498) hydrogen bonds : angle 4.34696 ( 4377) metal coordination : bond 0.00632 ( 5) metal coordination : angle 1.62165 ( 6) SS BOND : bond 0.00387 ( 2) SS BOND : angle 1.68330 ( 4) covalent geometry : bond 0.00340 (27879) covalent geometry : angle 0.56760 (37620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 3.011 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 356 LEU cc_start: 0.9147 (tp) cc_final: 0.8825 (pp) REVERT: A 513 GLN cc_start: 0.9571 (tt0) cc_final: 0.9318 (tm-30) REVERT: B 170 MET cc_start: 0.8624 (ppp) cc_final: 0.7980 (ppp) REVERT: B 188 MET cc_start: 0.8818 (tmm) cc_final: 0.8439 (tmm) REVERT: B 190 MET cc_start: 0.9405 (mtm) cc_final: 0.8981 (mtt) REVERT: B 225 MET cc_start: 0.6606 (ptp) cc_final: 0.6185 (tmm) REVERT: B 755 ASP cc_start: 0.9420 (m-30) cc_final: 0.8972 (t0) REVERT: B 891 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8951 (pp20) REVERT: B 1048 LYS cc_start: 0.8782 (tttt) cc_final: 0.8478 (tptt) REVERT: C 189 MET cc_start: -0.4103 (mmt) cc_final: -0.5297 (tpp) REVERT: C 315 PHE cc_start: 0.8863 (m-80) cc_final: 0.8517 (m-80) REVERT: C 343 MET cc_start: 0.1486 (mpp) cc_final: 0.1202 (mmt) REVERT: C 595 MET cc_start: 0.5610 (mtp) cc_final: 0.4667 (mmm) REVERT: C 617 MET cc_start: -0.4590 (mmp) cc_final: -0.4995 (ptp) REVERT: C 716 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7632 (mtp85) REVERT: C 719 TYR cc_start: 0.8074 (t80) cc_final: 0.7439 (t80) REVERT: C 796 MET cc_start: 0.7433 (mpp) cc_final: 0.6579 (tmm) REVERT: C 868 ASP cc_start: 0.9346 (p0) cc_final: 0.8854 (m-30) REVERT: C 940 MET cc_start: 0.8595 (mmp) cc_final: 0.8313 (mmp) REVERT: C 1033 ASN cc_start: 0.9492 (m-40) cc_final: 0.9237 (p0) REVERT: C 1256 MET cc_start: 0.9511 (tpt) cc_final: 0.8951 (tpp) REVERT: F 144 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8690 (mp0) outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.3944 time to fit residues: 120.9567 Evaluate side-chains 142 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 254 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B1190 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN C1107 ASN C1189 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.048154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.033243 restraints weight = 375768.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.033993 restraints weight = 280246.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.034494 restraints weight = 225593.267| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27886 Z= 0.161 Angle : 0.565 9.800 37630 Z= 0.304 Chirality : 0.041 0.162 4133 Planarity : 0.003 0.054 4858 Dihedral : 4.219 27.071 3656 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 0.23 % Allowed : 3.92 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3379 helix: 1.52 (0.12), residues: 1702 sheet: 0.29 (0.22), residues: 586 loop : -1.80 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS A 392 PHE 0.032 0.002 PHE B1071 TYR 0.030 0.001 TYR A 641 ARG 0.007 0.001 ARG B1021 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1498) hydrogen bonds : angle 4.15228 ( 4377) metal coordination : bond 0.00830 ( 5) metal coordination : angle 2.44727 ( 6) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.32390 ( 4) covalent geometry : bond 0.00341 (27879) covalent geometry : angle 0.56393 (37620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 3.217 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 209 LEU cc_start: 0.9768 (tp) cc_final: 0.9498 (tp) REVERT: A 356 LEU cc_start: 0.9214 (tp) cc_final: 0.8876 (pp) REVERT: B 170 MET cc_start: 0.8827 (ppp) cc_final: 0.8229 (ppp) REVERT: B 188 MET cc_start: 0.8775 (tmm) cc_final: 0.8311 (tmm) REVERT: B 190 MET cc_start: 0.9356 (mtm) cc_final: 0.8971 (mtt) REVERT: B 755 ASP cc_start: 0.9488 (m-30) cc_final: 0.8927 (t0) REVERT: B 759 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.8774 (pm20) REVERT: B 891 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8398 (mm-30) REVERT: B 958 MET cc_start: 0.8266 (tpp) cc_final: 0.8013 (tpp) REVERT: B 1048 LYS cc_start: 0.8934 (tttt) cc_final: 0.8643 (tptt) REVERT: C 189 MET cc_start: -0.3795 (mmt) cc_final: -0.5090 (mmt) REVERT: C 595 MET cc_start: 0.5833 (mtp) cc_final: 0.4998 (mmm) REVERT: C 617 MET cc_start: -0.4639 (mmp) cc_final: -0.5124 (ptp) REVERT: C 719 TYR cc_start: 0.8348 (t80) cc_final: 0.7757 (t80) REVERT: C 796 MET cc_start: 0.7977 (mpp) cc_final: 0.7624 (tmm) REVERT: C 868 ASP cc_start: 0.9360 (p0) cc_final: 0.8958 (t0) REVERT: C 940 MET cc_start: 0.8636 (mmp) cc_final: 0.8386 (mmp) REVERT: C 1033 ASN cc_start: 0.9583 (m-40) cc_final: 0.9372 (p0) REVERT: C 1256 MET cc_start: 0.9504 (tpt) cc_final: 0.8904 (tpp) REVERT: F 144 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8746 (mp0) outliers start: 7 outliers final: 1 residues processed: 173 average time/residue: 0.3977 time to fit residues: 112.4587 Evaluate side-chains 134 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 291 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 253 optimal weight: 40.0000 chunk 116 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 547 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS B 664 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1020 GLN C 35 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN C 936 ASN C 972 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.045865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031128 restraints weight = 386618.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.031828 restraints weight = 285162.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.032278 restraints weight = 228558.031| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27886 Z= 0.209 Angle : 0.630 10.493 37630 Z= 0.337 Chirality : 0.042 0.161 4133 Planarity : 0.004 0.054 4858 Dihedral : 4.515 31.711 3656 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3379 helix: 1.32 (0.12), residues: 1702 sheet: 0.16 (0.21), residues: 573 loop : -1.83 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C1219 HIS 0.013 0.002 HIS A 548 PHE 0.048 0.002 PHE C 48 TYR 0.017 0.002 TYR C 709 ARG 0.006 0.001 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1498) hydrogen bonds : angle 4.28728 ( 4377) metal coordination : bond 0.01028 ( 5) metal coordination : angle 3.15589 ( 6) SS BOND : bond 0.00436 ( 2) SS BOND : angle 2.46484 ( 4) covalent geometry : bond 0.00442 (27879) covalent geometry : angle 0.62878 (37620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 3.229 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: A 209 LEU cc_start: 0.9793 (tp) cc_final: 0.9456 (tp) REVERT: B 170 MET cc_start: 0.8984 (ppp) cc_final: 0.8341 (ppp) REVERT: B 246 MET cc_start: 0.8648 (tpt) cc_final: 0.8344 (tpp) REVERT: B 760 MET cc_start: 0.9667 (tmm) cc_final: 0.9453 (tmm) REVERT: B 891 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8505 (mm-30) REVERT: B 955 MET cc_start: 0.9402 (tmm) cc_final: 0.9148 (tmm) REVERT: C 189 MET cc_start: -0.3394 (mmt) cc_final: -0.4630 (mmt) REVERT: C 295 MET cc_start: 0.3981 (ptp) cc_final: 0.3626 (ptt) REVERT: C 595 MET cc_start: 0.5898 (mtp) cc_final: 0.5125 (mmm) REVERT: C 617 MET cc_start: -0.4065 (mmp) cc_final: -0.4953 (ptp) REVERT: C 796 MET cc_start: 0.8252 (mpp) cc_final: 0.7709 (tmm) REVERT: C 868 ASP cc_start: 0.9229 (p0) cc_final: 0.8961 (t0) REVERT: C 940 MET cc_start: 0.8589 (mmp) cc_final: 0.8350 (mmp) REVERT: C 1130 MET cc_start: 0.8790 (ppp) cc_final: 0.8244 (ppp) REVERT: C 1256 MET cc_start: 0.9534 (tpt) cc_final: 0.8952 (tpp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.4001 time to fit residues: 98.9371 Evaluate side-chains 114 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 19 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 206 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 708 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 881 ASN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 ASN ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN F 7 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.042997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.028647 restraints weight = 382856.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029294 restraints weight = 282463.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029738 restraints weight = 228141.230| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 27886 Z= 0.274 Angle : 0.739 9.565 37630 Z= 0.395 Chirality : 0.045 0.174 4133 Planarity : 0.005 0.058 4858 Dihedral : 5.002 33.645 3656 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.67 % Rotamer: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3379 helix: 0.74 (0.12), residues: 1699 sheet: -0.04 (0.21), residues: 576 loop : -1.88 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 691 HIS 0.022 0.002 HIS A 548 PHE 0.045 0.003 PHE A 568 TYR 0.021 0.002 TYR B 813 ARG 0.011 0.001 ARG B 722 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1498) hydrogen bonds : angle 4.73776 ( 4377) metal coordination : bond 0.01261 ( 5) metal coordination : angle 4.62354 ( 6) SS BOND : bond 0.00469 ( 2) SS BOND : angle 1.38659 ( 4) covalent geometry : bond 0.00570 (27879) covalent geometry : angle 0.73677 (37620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 4.122 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: B 170 MET cc_start: 0.9316 (ppp) cc_final: 0.8750 (ppp) REVERT: B 760 MET cc_start: 0.9591 (tmm) cc_final: 0.9369 (tmm) REVERT: B 955 MET cc_start: 0.9406 (tmm) cc_final: 0.9184 (tmm) REVERT: B 958 MET cc_start: 0.8649 (tpp) cc_final: 0.8378 (tpp) REVERT: C 189 MET cc_start: -0.2927 (mmt) cc_final: -0.3573 (mtt) REVERT: C 295 MET cc_start: 0.4431 (ptp) cc_final: 0.4188 (ptm) REVERT: C 595 MET cc_start: 0.6427 (mtp) cc_final: 0.5484 (mmm) REVERT: C 617 MET cc_start: -0.4486 (mmp) cc_final: -0.5381 (ptp) REVERT: C 796 MET cc_start: 0.8521 (mpp) cc_final: 0.8158 (tmm) REVERT: C 868 ASP cc_start: 0.9344 (p0) cc_final: 0.9081 (t0) REVERT: C 905 MET cc_start: 0.9285 (mtm) cc_final: 0.9016 (mtp) REVERT: C 940 MET cc_start: 0.8616 (mmp) cc_final: 0.8382 (mmp) REVERT: C 1130 MET cc_start: 0.9039 (ppp) cc_final: 0.8638 (ppp) REVERT: C 1142 MET cc_start: 0.9252 (tpt) cc_final: 0.9052 (tpp) REVERT: C 1256 MET cc_start: 0.9593 (tpt) cc_final: 0.9007 (tpp) REVERT: F 144 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8828 (mp0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.4640 time to fit residues: 99.7496 Evaluate side-chains 102 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 107 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 439 ASN A 469 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 GLN ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.043006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.030886 restraints weight = 409837.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.031560 restraints weight = 285773.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.032141 restraints weight = 221553.724| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27886 Z= 0.159 Angle : 0.587 10.162 37630 Z= 0.317 Chirality : 0.042 0.147 4133 Planarity : 0.004 0.057 4858 Dihedral : 4.744 32.718 3656 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3379 helix: 1.07 (0.12), residues: 1699 sheet: 0.01 (0.22), residues: 578 loop : -1.77 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 106 HIS 0.009 0.001 HIS A 548 PHE 0.023 0.002 PHE C 45 TYR 0.019 0.001 TYR C 833 ARG 0.006 0.001 ARG C 843 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1498) hydrogen bonds : angle 4.43078 ( 4377) metal coordination : bond 0.00804 ( 5) metal coordination : angle 2.63564 ( 6) SS BOND : bond 0.00451 ( 2) SS BOND : angle 0.87187 ( 4) covalent geometry : bond 0.00335 (27879) covalent geometry : angle 0.58641 (37620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 3.355 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: B 170 MET cc_start: 0.9300 (ppp) cc_final: 0.8634 (ppp) REVERT: B 760 MET cc_start: 0.9599 (tmm) cc_final: 0.9356 (tmm) REVERT: B 955 MET cc_start: 0.9410 (tmm) cc_final: 0.9179 (tmm) REVERT: C 189 MET cc_start: -0.6388 (mmt) cc_final: -0.6741 (mtt) REVERT: C 230 MET cc_start: 0.3890 (mmt) cc_final: 0.3537 (mmt) REVERT: C 295 MET cc_start: 0.5421 (ptp) cc_final: 0.5213 (ptm) REVERT: C 595 MET cc_start: 0.6576 (mtp) cc_final: 0.6170 (mtm) REVERT: C 617 MET cc_start: -0.4492 (mmp) cc_final: -0.5003 (ptp) REVERT: C 697 TYR cc_start: 0.8919 (m-80) cc_final: 0.8636 (m-80) REVERT: C 796 MET cc_start: 0.8643 (mpp) cc_final: 0.8202 (tmm) REVERT: C 868 ASP cc_start: 0.9416 (p0) cc_final: 0.9158 (t0) REVERT: C 905 MET cc_start: 0.9263 (mtm) cc_final: 0.9048 (mtp) REVERT: C 940 MET cc_start: 0.8631 (mmp) cc_final: 0.8403 (mmp) REVERT: C 1130 MET cc_start: 0.9023 (ppp) cc_final: 0.8658 (ppp) REVERT: C 1256 MET cc_start: 0.9659 (tpt) cc_final: 0.9161 (tpp) REVERT: F 144 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8919 (tt0) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.3931 time to fit residues: 83.3895 Evaluate side-chains 106 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 141 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 641 ASN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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 = 0.3410 r_free = 0.3410 target = 0.043599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.029140 restraints weight = 387804.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.029775 restraints weight = 278628.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.030365 restraints weight = 222019.840| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27886 Z= 0.150 Angle : 0.576 9.637 37630 Z= 0.310 Chirality : 0.042 0.187 4133 Planarity : 0.003 0.054 4858 Dihedral : 4.621 32.516 3656 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3379 helix: 1.14 (0.12), residues: 1708 sheet: 0.07 (0.22), residues: 580 loop : -1.71 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 582 HIS 0.008 0.001 HIS A 548 PHE 0.022 0.002 PHE C 45 TYR 0.019 0.001 TYR C 175 ARG 0.006 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1498) hydrogen bonds : angle 4.33196 ( 4377) metal coordination : bond 0.00641 ( 5) metal coordination : angle 2.51655 ( 6) SS BOND : bond 0.00451 ( 2) SS BOND : angle 0.86369 ( 4) covalent geometry : bond 0.00317 (27879) covalent geometry : angle 0.57540 (37620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 3.528 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: B 170 MET cc_start: 0.9280 (ppp) cc_final: 0.8598 (ppp) REVERT: B 673 MET cc_start: 0.9271 (ptm) cc_final: 0.8951 (ptp) REVERT: B 760 MET cc_start: 0.9603 (tmm) cc_final: 0.9363 (tmm) REVERT: B 955 MET cc_start: 0.9437 (tmm) cc_final: 0.9184 (tmm) REVERT: B 1159 MET cc_start: 0.5215 (tpp) cc_final: 0.4903 (tpp) REVERT: C 189 MET cc_start: -0.3436 (mmt) cc_final: -0.4141 (mtt) REVERT: C 230 MET cc_start: 0.4166 (mmt) cc_final: 0.3770 (mmt) REVERT: C 595 MET cc_start: 0.6574 (mtp) cc_final: 0.6159 (mtm) REVERT: C 617 MET cc_start: -0.4356 (mmp) cc_final: -0.5087 (ptp) REVERT: C 697 TYR cc_start: 0.8905 (m-80) cc_final: 0.8593 (m-80) REVERT: C 796 MET cc_start: 0.8705 (mpp) cc_final: 0.8245 (tmm) REVERT: C 868 ASP cc_start: 0.9336 (p0) cc_final: 0.9094 (t0) REVERT: C 905 MET cc_start: 0.9215 (mtm) cc_final: 0.8983 (mtp) REVERT: C 940 MET cc_start: 0.8738 (mmp) cc_final: 0.8478 (mmp) REVERT: C 1130 MET cc_start: 0.9024 (ppp) cc_final: 0.8619 (ppp) REVERT: C 1256 MET cc_start: 0.9642 (tpt) cc_final: 0.9139 (tpp) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.5225 time to fit residues: 115.4802 Evaluate side-chains 105 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 167 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 312 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 208 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 477 GLN C 534 ASN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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 = 0.3402 r_free = 0.3402 target = 0.043398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.029296 restraints weight = 384399.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.030250 restraints weight = 300555.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.030048 restraints weight = 231835.267| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27886 Z= 0.143 Angle : 0.574 10.936 37630 Z= 0.307 Chirality : 0.042 0.177 4133 Planarity : 0.003 0.053 4858 Dihedral : 4.555 32.299 3656 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3379 helix: 1.22 (0.12), residues: 1709 sheet: 0.12 (0.22), residues: 570 loop : -1.69 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1013 HIS 0.007 0.001 HIS A 548 PHE 0.021 0.001 PHE C 45 TYR 0.025 0.001 TYR C 833 ARG 0.003 0.000 ARG C 843 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1498) hydrogen bonds : angle 4.29874 ( 4377) metal coordination : bond 0.00579 ( 5) metal coordination : angle 2.31094 ( 6) SS BOND : bond 0.00430 ( 2) SS BOND : angle 0.85460 ( 4) covalent geometry : bond 0.00305 (27879) covalent geometry : angle 0.57344 (37620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.9224 (ppp) cc_final: 0.8498 (ppp) REVERT: B 246 MET cc_start: 0.7922 (tpt) cc_final: 0.7544 (tpt) REVERT: B 673 MET cc_start: 0.9337 (ptm) cc_final: 0.9053 (ptp) REVERT: B 760 MET cc_start: 0.9604 (tmm) cc_final: 0.9389 (tmm) REVERT: B 958 MET cc_start: 0.8278 (tpp) cc_final: 0.8053 (tpp) REVERT: B 1159 MET cc_start: 0.5263 (tpp) cc_final: 0.4980 (tpp) REVERT: C 27 TRP cc_start: 0.5378 (m100) cc_final: 0.5061 (m100) REVERT: C 189 MET cc_start: -0.4880 (mmt) cc_final: -0.5569 (mmt) REVERT: C 230 MET cc_start: 0.4073 (mmt) cc_final: 0.3671 (mmt) REVERT: C 292 MET cc_start: 0.0836 (mmm) cc_final: 0.0540 (mmt) REVERT: C 595 MET cc_start: 0.6520 (mtp) cc_final: 0.6092 (mtm) REVERT: C 617 MET cc_start: -0.4219 (mmp) cc_final: -0.4920 (ptp) REVERT: C 697 TYR cc_start: 0.8932 (m-80) cc_final: 0.8558 (m-80) REVERT: C 796 MET cc_start: 0.8693 (mpp) cc_final: 0.8137 (tmm) REVERT: C 868 ASP cc_start: 0.9376 (p0) cc_final: 0.9112 (t0) REVERT: C 905 MET cc_start: 0.9232 (mtm) cc_final: 0.8989 (mtp) REVERT: C 940 MET cc_start: 0.8766 (mmp) cc_final: 0.8515 (mmp) REVERT: C 1130 MET cc_start: 0.8978 (ppp) cc_final: 0.8603 (ppp) REVERT: C 1256 MET cc_start: 0.9668 (tpt) cc_final: 0.9165 (tpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4602 time to fit residues: 96.4625 Evaluate side-chains 104 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 253 optimal weight: 30.0000 chunk 204 optimal weight: 0.2980 chunk 106 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 271 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.043171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.028823 restraints weight = 386847.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.029529 restraints weight = 280438.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.029964 restraints weight = 223595.773| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27886 Z= 0.142 Angle : 0.572 9.850 37630 Z= 0.306 Chirality : 0.042 0.166 4133 Planarity : 0.003 0.052 4858 Dihedral : 4.494 32.286 3656 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3379 helix: 1.29 (0.12), residues: 1709 sheet: 0.16 (0.22), residues: 569 loop : -1.66 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C1219 HIS 0.006 0.001 HIS A 548 PHE 0.021 0.001 PHE C 45 TYR 0.020 0.001 TYR C 175 ARG 0.014 0.000 ARG B 754 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1498) hydrogen bonds : angle 4.27546 ( 4377) metal coordination : bond 0.00529 ( 5) metal coordination : angle 2.18261 ( 6) SS BOND : bond 0.00393 ( 2) SS BOND : angle 1.02042 ( 4) covalent geometry : bond 0.00299 (27879) covalent geometry : angle 0.57180 (37620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.9232 (ppp) cc_final: 0.8503 (ppp) REVERT: B 261 MET cc_start: 0.8326 (tpp) cc_final: 0.8122 (mmm) REVERT: B 673 MET cc_start: 0.9309 (ptm) cc_final: 0.9038 (ptp) REVERT: B 760 MET cc_start: 0.9548 (tmm) cc_final: 0.9277 (tmm) REVERT: B 958 MET cc_start: 0.8334 (tpp) cc_final: 0.8118 (tpp) REVERT: B 1159 MET cc_start: 0.5198 (tpp) cc_final: 0.4887 (tpp) REVERT: C 189 MET cc_start: -0.3676 (mmt) cc_final: -0.4386 (mmt) REVERT: C 230 MET cc_start: 0.4496 (mmt) cc_final: 0.4061 (mmt) REVERT: C 292 MET cc_start: 0.1624 (mmm) cc_final: 0.1306 (mmt) REVERT: C 595 MET cc_start: 0.6793 (mtp) cc_final: 0.6431 (mtm) REVERT: C 617 MET cc_start: -0.4655 (mmp) cc_final: -0.5090 (ptp) REVERT: C 796 MET cc_start: 0.8778 (mpp) cc_final: 0.8176 (tmm) REVERT: C 905 MET cc_start: 0.9212 (mtm) cc_final: 0.8989 (mtp) REVERT: C 940 MET cc_start: 0.8769 (mmp) cc_final: 0.8512 (mmp) REVERT: C 1130 MET cc_start: 0.9030 (ppp) cc_final: 0.8619 (ppp) REVERT: C 1142 MET cc_start: 0.9289 (mmp) cc_final: 0.8891 (mmm) REVERT: C 1256 MET cc_start: 0.9659 (tpt) cc_final: 0.9117 (tpp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3690 time to fit residues: 77.7542 Evaluate side-chains 103 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 113 optimal weight: 6.9990 chunk 65 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 268 optimal weight: 0.6980 overall best weight: 2.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 345 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.043011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.028960 restraints weight = 383566.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.029928 restraints weight = 297171.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029798 restraints weight = 219801.193| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27886 Z= 0.138 Angle : 0.580 10.408 37630 Z= 0.309 Chirality : 0.042 0.168 4133 Planarity : 0.003 0.051 4858 Dihedral : 4.484 32.073 3656 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3379 helix: 1.30 (0.12), residues: 1709 sheet: 0.07 (0.22), residues: 585 loop : -1.67 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 214 HIS 0.006 0.001 HIS A 548 PHE 0.020 0.001 PHE C 45 TYR 0.027 0.001 TYR C 833 ARG 0.003 0.000 ARG B 840 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 1498) hydrogen bonds : angle 4.29901 ( 4377) metal coordination : bond 0.00526 ( 5) metal coordination : angle 2.39640 ( 6) SS BOND : bond 0.00435 ( 2) SS BOND : angle 0.92154 ( 4) covalent geometry : bond 0.00292 (27879) covalent geometry : angle 0.57938 (37620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.9199 (ppp) cc_final: 0.8818 (ppp) REVERT: B 261 MET cc_start: 0.8411 (tpp) cc_final: 0.8181 (mmm) REVERT: B 673 MET cc_start: 0.9314 (ptm) cc_final: 0.9051 (ptp) REVERT: B 760 MET cc_start: 0.9556 (tmm) cc_final: 0.9228 (tmm) REVERT: B 958 MET cc_start: 0.8362 (tpp) cc_final: 0.8116 (tpp) REVERT: B 1159 MET cc_start: 0.5177 (tpp) cc_final: 0.4937 (tpp) REVERT: C 189 MET cc_start: -0.5255 (mmt) cc_final: -0.5886 (mmt) REVERT: C 230 MET cc_start: 0.4413 (mmt) cc_final: 0.3965 (mmt) REVERT: C 292 MET cc_start: 0.1638 (mmm) cc_final: 0.1341 (mmt) REVERT: C 595 MET cc_start: 0.6659 (mtp) cc_final: 0.6285 (mtm) REVERT: C 617 MET cc_start: -0.4231 (mmp) cc_final: -0.4876 (ptp) REVERT: C 796 MET cc_start: 0.8846 (mpp) cc_final: 0.8259 (tmm) REVERT: C 905 MET cc_start: 0.9258 (mtm) cc_final: 0.9044 (mtp) REVERT: C 940 MET cc_start: 0.8824 (mmp) cc_final: 0.8605 (mmp) REVERT: C 1130 MET cc_start: 0.9027 (ppp) cc_final: 0.8642 (ppp) REVERT: C 1142 MET cc_start: 0.9317 (mmp) cc_final: 0.9018 (mmm) REVERT: C 1256 MET cc_start: 0.9667 (tpt) cc_final: 0.9127 (tpp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3654 time to fit residues: 75.5403 Evaluate side-chains 100 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 139 optimal weight: 0.9990 chunk 217 optimal weight: 30.0000 chunk 296 optimal weight: 0.0020 chunk 39 optimal weight: 30.0000 chunk 173 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 231 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.043029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.029046 restraints weight = 385274.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.030030 restraints weight = 304998.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.029861 restraints weight = 221555.772| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27886 Z= 0.126 Angle : 0.568 10.157 37630 Z= 0.303 Chirality : 0.042 0.164 4133 Planarity : 0.003 0.050 4858 Dihedral : 4.426 32.049 3656 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3379 helix: 1.36 (0.12), residues: 1708 sheet: 0.11 (0.22), residues: 585 loop : -1.65 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 214 HIS 0.005 0.001 HIS A 548 PHE 0.020 0.001 PHE C 45 TYR 0.020 0.001 TYR C 175 ARG 0.003 0.000 ARG C 400 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1498) hydrogen bonds : angle 4.25212 ( 4377) metal coordination : bond 0.00422 ( 5) metal coordination : angle 1.92946 ( 6) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.04768 ( 4) covalent geometry : bond 0.00268 (27879) covalent geometry : angle 0.56786 (37620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10182.51 seconds wall clock time: 182 minutes 1.69 seconds (10921.69 seconds total)