Starting phenix.real_space_refine on Mon Aug 25 11:30:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmd_34896/08_2025/8hmd_34896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmd_34896/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hmd_34896/08_2025/8hmd_34896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmd_34896/08_2025/8hmd_34896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmd_34896/08_2025/8hmd_34896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmd_34896/08_2025/8hmd_34896.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.81, per 1000 atoms: 0.21 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.08 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: 4.85 Time building geometry restraints manager: 2.84 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.190 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- 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 : 9.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 266 TYR 0.023 0.001 TYR C 21 PHE 0.037 0.001 PHE C 48 TRP 0.037 0.001 TRP B 164 HIS 0.006 0.001 HIS B1014 Details of bonding type rmsd covalent geometry : bond 0.00257 (27879) covalent geometry : angle 0.61910 (37620) SS BOND : bond 0.00420 ( 2) SS BOND : angle 3.31538 ( 4) hydrogen bonds : bond 0.12574 ( 1498) hydrogen bonds : angle 5.29329 ( 4377) metal coordination : bond 0.00138 ( 5) metal coordination : angle 1.59373 ( 6) *********************** 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 : 1.032 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: 0.1775 time to fit residues: 82.5646 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 : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 9.9990 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 96 ASN A 410 HIS ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN ** 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 ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN ** B 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B1020 GLN B1061 ASN B1188 ASN B1193 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 131 HIS ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN C 855 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1189 GLN C1331 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.048092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033062 restraints weight = 369329.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033743 restraints weight = 277866.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.034327 restraints weight = 225550.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.034618 restraints weight = 192464.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.034966 restraints weight = 171626.704| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 27886 Z= 0.230 Angle : 0.682 9.405 37630 Z= 0.361 Chirality : 0.044 0.234 4133 Planarity : 0.004 0.058 4858 Dihedral : 4.450 26.862 3656 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 0.47 % Allowed : 4.45 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.14), residues: 3379 helix: 1.26 (0.12), residues: 1701 sheet: 0.07 (0.21), residues: 590 loop : -1.91 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 753 TYR 0.020 0.002 TYR B 813 PHE 0.020 0.002 PHE C 45 TRP 0.022 0.002 TRP B 767 HIS 0.009 0.002 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00475 (27879) covalent geometry : angle 0.68099 (37620) SS BOND : bond 0.00489 ( 2) SS BOND : angle 1.99710 ( 4) hydrogen bonds : bond 0.04001 ( 1498) hydrogen bonds : angle 4.45410 ( 4377) metal coordination : bond 0.00965 ( 5) metal coordination : angle 3.27401 ( 6) *********************** 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 182 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.819 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: 0.9800 (tp) cc_final: 0.9598 (tp) REVERT: A 356 LEU cc_start: 0.9255 (tp) cc_final: 0.8899 (pp) REVERT: B 170 MET cc_start: 0.8644 (ppp) cc_final: 0.8019 (ppp) REVERT: B 188 MET cc_start: 0.8831 (tmm) cc_final: 0.8416 (tmm) REVERT: B 190 MET cc_start: 0.9388 (mtm) cc_final: 0.9014 (mtt) REVERT: B 225 MET cc_start: 0.6836 (ptp) cc_final: 0.6318 (tmm) REVERT: B 755 ASP cc_start: 0.9433 (m-30) cc_final: 0.9016 (t0) REVERT: B 760 MET cc_start: 0.9693 (tmm) cc_final: 0.9493 (tmm) REVERT: B 797 GLU cc_start: 0.9496 (OUTLIER) cc_final: 0.9219 (pm20) REVERT: B 958 MET cc_start: 0.8371 (tpp) cc_final: 0.8150 (tpp) REVERT: B 1048 LYS cc_start: 0.8942 (tttt) cc_final: 0.8681 (tptt) REVERT: C 189 MET cc_start: -0.3797 (mmt) cc_final: -0.4877 (mmt) REVERT: C 595 MET cc_start: 0.5568 (mtp) cc_final: 0.4613 (mmm) REVERT: C 617 MET cc_start: -0.4422 (mmp) cc_final: -0.4986 (ptp) REVERT: C 716 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7937 (ptp-170) REVERT: C 719 TYR cc_start: 0.8242 (t80) cc_final: 0.7697 (t80) REVERT: C 796 MET cc_start: 0.7533 (mpp) cc_final: 0.6939 (tmm) REVERT: C 868 ASP cc_start: 0.9320 (p0) cc_final: 0.8923 (t0) REVERT: C 940 MET cc_start: 0.8578 (mmp) cc_final: 0.8303 (mmp) REVERT: C 1256 MET cc_start: 0.9539 (tpt) cc_final: 0.8918 (tpp) REVERT: F 144 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8769 (mp0) outliers start: 14 outliers final: 2 residues processed: 182 average time/residue: 0.1716 time to fit residues: 50.1912 Evaluate side-chains 138 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 241 optimal weight: 30.0000 chunk 246 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 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 664 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN B 908 GLN B1190 ASN C 31 GLN C 35 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 415 GLN C 530 GLN C 855 ASN C 881 GLN C 972 ASN C1107 ASN C1331 GLN F 27 GLN F 117 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.045317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.033154 restraints weight = 396770.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.033824 restraints weight = 282356.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.034300 restraints weight = 221352.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.034300 restraints weight = 183716.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.034300 restraints weight = 183716.493| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27886 Z= 0.211 Angle : 0.620 8.638 37630 Z= 0.339 Chirality : 0.042 0.157 4133 Planarity : 0.004 0.065 4858 Dihedral : 4.549 30.534 3656 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 0.30 % Allowed : 4.55 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3379 helix: 1.21 (0.12), residues: 1712 sheet: 0.16 (0.21), residues: 570 loop : -1.85 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 722 TYR 0.025 0.002 TYR C 697 PHE 0.032 0.002 PHE B1071 TRP 0.012 0.002 TRP A 25 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00432 (27879) covalent geometry : angle 0.61780 (37620) SS BOND : bond 0.01696 ( 2) SS BOND : angle 2.03747 ( 4) hydrogen bonds : bond 0.03947 ( 1498) hydrogen bonds : angle 4.34587 ( 4377) metal coordination : bond 0.01049 ( 5) metal coordination : angle 3.34718 ( 6) *********************** 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 164 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.929 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: B 170 MET cc_start: 0.8838 (ppp) cc_final: 0.8292 (ppp) REVERT: B 188 MET cc_start: 0.8687 (tmm) cc_final: 0.8277 (tmm) REVERT: B 190 MET cc_start: 0.9358 (mtm) cc_final: 0.8913 (mtt) REVERT: B 543 MET cc_start: 0.8502 (tpt) cc_final: 0.8293 (tpt) REVERT: B 790 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8759 (pm20) REVERT: B 958 MET cc_start: 0.8478 (tpp) cc_final: 0.8258 (tpp) REVERT: C 189 MET cc_start: -0.6545 (mmt) cc_final: -0.7271 (mmt) REVERT: C 595 MET cc_start: 0.5912 (mtp) cc_final: 0.5136 (mmm) REVERT: C 617 MET cc_start: -0.4131 (mmp) cc_final: -0.5125 (ptp) REVERT: C 719 TYR cc_start: 0.8623 (t80) cc_final: 0.8079 (t80) REVERT: C 796 MET cc_start: 0.8183 (mpp) cc_final: 0.7778 (tmm) REVERT: C 868 ASP cc_start: 0.9359 (p0) cc_final: 0.9014 (t0) REVERT: C 940 MET cc_start: 0.8601 (mmp) cc_final: 0.8331 (mmp) REVERT: C 1130 MET cc_start: 0.8737 (ppp) cc_final: 0.8523 (ppp) REVERT: C 1256 MET cc_start: 0.9558 (tpt) cc_final: 0.9041 (tpp) REVERT: F 144 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8751 (mp0) outliers start: 9 outliers final: 1 residues processed: 164 average time/residue: 0.1592 time to fit residues: 42.7340 Evaluate side-chains 114 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 469 ASN A 527 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** 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 322 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 ASN C 946 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 37 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.044446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029903 restraints weight = 387728.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.030597 restraints weight = 285004.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.031021 restraints weight = 228516.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.031403 restraints weight = 195500.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031546 restraints weight = 174297.135| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27886 Z= 0.219 Angle : 0.645 13.554 37630 Z= 0.344 Chirality : 0.043 0.168 4133 Planarity : 0.004 0.054 4858 Dihedral : 4.654 32.610 3656 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3379 helix: 1.08 (0.12), residues: 1710 sheet: 0.02 (0.21), residues: 578 loop : -1.83 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 455 TYR 0.021 0.002 TYR C 709 PHE 0.047 0.002 PHE C 48 TRP 0.016 0.002 TRP C1219 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00456 (27879) covalent geometry : angle 0.64353 (37620) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.10523 ( 4) hydrogen bonds : bond 0.03769 ( 1498) hydrogen bonds : angle 4.41472 ( 4377) metal coordination : bond 0.00946 ( 5) metal coordination : angle 3.45208 ( 6) *********************** 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 139 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.885 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: B 170 MET cc_start: 0.8537 (ppp) cc_final: 0.8320 (ppp) REVERT: B 760 MET cc_start: 0.9712 (tmm) cc_final: 0.9488 (tmm) REVERT: B 958 MET cc_start: 0.8377 (tpp) cc_final: 0.7979 (tpp) REVERT: C 189 MET cc_start: -0.3305 (mmt) cc_final: -0.3981 (mtt) REVERT: C 377 MET cc_start: 0.5383 (ttp) cc_final: 0.4890 (tmm) REVERT: C 595 MET cc_start: 0.6133 (mtp) cc_final: 0.5314 (mmm) REVERT: C 617 MET cc_start: -0.4351 (mmp) cc_final: -0.5081 (ptp) REVERT: C 796 MET cc_start: 0.8362 (mpp) cc_final: 0.7810 (tmm) REVERT: C 868 ASP cc_start: 0.9265 (p0) cc_final: 0.8996 (t0) REVERT: C 940 MET cc_start: 0.8601 (mmp) cc_final: 0.8351 (mmp) REVERT: C 1130 MET cc_start: 0.9051 (ppp) cc_final: 0.8722 (ppp) REVERT: C 1256 MET cc_start: 0.9592 (tpt) cc_final: 0.8990 (tpp) REVERT: F 144 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8848 (mp0) outliers start: 3 outliers final: 2 residues processed: 139 average time/residue: 0.1582 time to fit residues: 36.4589 Evaluate side-chains 113 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 266 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 284 optimal weight: 30.0000 chunk 309 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 206 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 439 ASN A 596 GLN ** 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 704 ASN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 845 GLN B 881 ASN B1020 GLN B1061 ASN ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN C 387 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.042405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030265 restraints weight = 401748.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030967 restraints weight = 287966.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.031489 restraints weight = 222821.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.031869 restraints weight = 184027.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.032157 restraints weight = 159038.254| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27886 Z= 0.236 Angle : 0.655 10.589 37630 Z= 0.354 Chirality : 0.043 0.253 4133 Planarity : 0.004 0.054 4858 Dihedral : 4.832 31.352 3656 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3379 helix: 0.90 (0.12), residues: 1708 sheet: -0.04 (0.21), residues: 576 loop : -1.84 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 819 TYR 0.019 0.002 TYR B 813 PHE 0.025 0.002 PHE C1187 TRP 0.015 0.002 TRP B 582 HIS 0.015 0.002 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00490 (27879) covalent geometry : angle 0.65358 (37620) SS BOND : bond 0.00478 ( 2) SS BOND : angle 0.95593 ( 4) hydrogen bonds : bond 0.04028 ( 1498) hydrogen bonds : angle 4.55438 ( 4377) metal coordination : bond 0.01115 ( 5) metal coordination : angle 3.38668 ( 6) *********************** 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 125 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 1.073 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: B 170 MET cc_start: 0.8935 (ppp) cc_final: 0.8561 (ppp) REVERT: B 958 MET cc_start: 0.8377 (tpp) cc_final: 0.8081 (tpp) REVERT: C 27 TRP cc_start: 0.6285 (m-90) cc_final: 0.6026 (m100) REVERT: C 189 MET cc_start: -0.6282 (mmt) cc_final: -0.6691 (mtt) REVERT: C 595 MET cc_start: 0.6511 (mtp) cc_final: 0.5640 (mmm) REVERT: C 617 MET cc_start: -0.4349 (mmp) cc_final: -0.5086 (ptp) REVERT: C 796 MET cc_start: 0.8636 (mpp) cc_final: 0.8116 (tmm) REVERT: C 868 ASP cc_start: 0.9389 (p0) cc_final: 0.9114 (t0) REVERT: C 905 MET cc_start: 0.9259 (mtm) cc_final: 0.9033 (mtp) REVERT: C 940 MET cc_start: 0.8606 (mmp) cc_final: 0.8370 (mmp) REVERT: C 1092 MET cc_start: 0.8691 (ptp) cc_final: 0.8349 (ptp) REVERT: C 1130 MET cc_start: 0.9121 (ppp) cc_final: 0.8765 (tmm) REVERT: C 1142 MET cc_start: 0.9297 (tpt) cc_final: 0.9079 (tpp) REVERT: C 1256 MET cc_start: 0.9646 (tpt) cc_final: 0.9082 (tpp) REVERT: F 144 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8884 (tt0) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1860 time to fit residues: 39.1986 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 : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 177 optimal weight: 2.9990 chunk 233 optimal weight: 30.0000 chunk 281 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** B1061 ASN ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.043317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.028934 restraints weight = 385041.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.029514 restraints weight = 278836.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.029974 restraints weight = 222543.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.030163 restraints weight = 189590.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.030559 restraints weight = 174361.923| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27886 Z= 0.166 Angle : 0.580 8.394 37630 Z= 0.314 Chirality : 0.042 0.155 4133 Planarity : 0.004 0.057 4858 Dihedral : 4.696 32.007 3656 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3379 helix: 1.06 (0.12), residues: 1710 sheet: -0.00 (0.22), residues: 579 loop : -1.76 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1058 TYR 0.022 0.001 TYR C 833 PHE 0.022 0.002 PHE C 45 TRP 0.014 0.001 TRP B 582 HIS 0.010 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00346 (27879) covalent geometry : angle 0.57830 (37620) SS BOND : bond 0.00405 ( 2) SS BOND : angle 0.81527 ( 4) hydrogen bonds : bond 0.03590 ( 1498) hydrogen bonds : angle 4.40108 ( 4377) metal coordination : bond 0.00867 ( 5) metal coordination : angle 3.74947 ( 6) *********************** 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 121 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8883 (ppp) cc_final: 0.8548 (ppp) REVERT: B 958 MET cc_start: 0.8321 (tpp) cc_final: 0.8087 (tpp) REVERT: C 27 TRP cc_start: 0.5937 (m-90) cc_final: 0.5735 (m100) REVERT: C 189 MET cc_start: -0.3033 (mmt) cc_final: -0.3732 (mtt) REVERT: C 292 MET cc_start: -0.0577 (tpp) cc_final: -0.1085 (mmt) REVERT: C 377 MET cc_start: 0.6245 (ptm) cc_final: 0.6040 (tmm) REVERT: C 595 MET cc_start: 0.6465 (mtp) cc_final: 0.6020 (mtm) REVERT: C 617 MET cc_start: -0.4394 (mmp) cc_final: -0.5135 (ptp) REVERT: C 697 TYR cc_start: 0.8864 (m-80) cc_final: 0.8612 (m-80) REVERT: C 796 MET cc_start: 0.8650 (mpp) cc_final: 0.8138 (tmm) REVERT: C 868 ASP cc_start: 0.9302 (p0) cc_final: 0.9054 (t0) REVERT: C 905 MET cc_start: 0.9228 (mtm) cc_final: 0.9002 (mtp) REVERT: C 940 MET cc_start: 0.8680 (mmp) cc_final: 0.8419 (mmp) REVERT: C 1130 MET cc_start: 0.9029 (ppp) cc_final: 0.8627 (ppp) REVERT: C 1256 MET cc_start: 0.9640 (tpt) cc_final: 0.9116 (tpp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1741 time to fit residues: 35.9044 Evaluate side-chains 101 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 217 optimal weight: 30.0000 chunk 245 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 181 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 ASN ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 589 GLN C 641 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 117 GLN ** 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 = 0.3390 r_free = 0.3390 target = 0.042974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028544 restraints weight = 384002.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029292 restraints weight = 277411.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.029702 restraints weight = 220905.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.030134 restraints weight = 189017.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.030279 restraints weight = 168829.272| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27886 Z= 0.163 Angle : 0.582 9.670 37630 Z= 0.314 Chirality : 0.042 0.179 4133 Planarity : 0.004 0.052 4858 Dihedral : 4.641 31.401 3656 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 3379 helix: 1.12 (0.12), residues: 1711 sheet: 0.03 (0.22), residues: 577 loop : -1.75 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1027 TYR 0.020 0.001 TYR C 175 PHE 0.022 0.002 PHE C 45 TRP 0.012 0.001 TRP B 582 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00343 (27879) covalent geometry : angle 0.58006 (37620) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.95107 ( 4) hydrogen bonds : bond 0.03536 ( 1498) hydrogen bonds : angle 4.35907 ( 4377) metal coordination : bond 0.01977 ( 5) metal coordination : angle 3.51108 ( 6) *********************** 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 118 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8933 (ppp) cc_final: 0.8533 (ppp) REVERT: B 225 MET cc_start: 0.6723 (ppp) cc_final: 0.6232 (ppp) REVERT: B 673 MET cc_start: 0.9025 (ptp) cc_final: 0.8533 (ptp) REVERT: B 760 MET cc_start: 0.9655 (tmm) cc_final: 0.9419 (tmm) REVERT: B 955 MET cc_start: 0.9475 (tmm) cc_final: 0.9244 (tmm) REVERT: B 1159 MET cc_start: 0.6305 (tpp) cc_final: 0.5752 (tpp) REVERT: C 27 TRP cc_start: 0.5874 (m-90) cc_final: 0.5663 (m100) REVERT: C 189 MET cc_start: -0.3339 (mmt) cc_final: -0.4063 (mmt) REVERT: C 377 MET cc_start: 0.6270 (ptm) cc_final: 0.5996 (tmm) REVERT: C 595 MET cc_start: 0.6514 (mtp) cc_final: 0.6095 (mtm) REVERT: C 617 MET cc_start: -0.4509 (mmp) cc_final: -0.5120 (ptp) REVERT: C 697 TYR cc_start: 0.8905 (m-80) cc_final: 0.8650 (m-80) REVERT: C 796 MET cc_start: 0.8692 (mpp) cc_final: 0.8108 (tmm) REVERT: C 905 MET cc_start: 0.9221 (mtm) cc_final: 0.8993 (mtp) REVERT: C 940 MET cc_start: 0.8767 (mmp) cc_final: 0.8510 (mmp) REVERT: C 1130 MET cc_start: 0.9079 (ppp) cc_final: 0.8661 (ppp) REVERT: C 1142 MET cc_start: 0.9142 (mmp) cc_final: 0.8717 (mmm) REVERT: C 1256 MET cc_start: 0.9642 (tpt) cc_final: 0.9112 (tpp) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1543 time to fit residues: 30.6810 Evaluate side-chains 100 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 101 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** 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 131 HIS ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** 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 = 0.3365 r_free = 0.3365 target = 0.042182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.027894 restraints weight = 381466.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.028578 restraints weight = 277205.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.029063 restraints weight = 222318.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029287 restraints weight = 189794.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.029621 restraints weight = 172643.139| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27886 Z= 0.201 Angle : 0.625 11.004 37630 Z= 0.336 Chirality : 0.043 0.190 4133 Planarity : 0.004 0.050 4858 Dihedral : 4.739 33.642 3656 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3379 helix: 1.02 (0.12), residues: 1710 sheet: -0.06 (0.22), residues: 575 loop : -1.75 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 843 TYR 0.021 0.002 TYR C 175 PHE 0.022 0.002 PHE C 45 TRP 0.023 0.002 TRP A 214 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00420 (27879) covalent geometry : angle 0.62241 (37620) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.62273 ( 4) hydrogen bonds : bond 0.03732 ( 1498) hydrogen bonds : angle 4.48864 ( 4377) metal coordination : bond 0.01533 ( 5) metal coordination : angle 4.00979 ( 6) *********************** 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 117 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8983 (ppp) cc_final: 0.8609 (ppp) REVERT: B 225 MET cc_start: 0.6974 (ppp) cc_final: 0.6599 (tmm) REVERT: B 673 MET cc_start: 0.9049 (ptp) cc_final: 0.8590 (ptp) REVERT: B 1159 MET cc_start: 0.6408 (tpp) cc_final: 0.6178 (tpp) REVERT: C 189 MET cc_start: -0.3786 (mmt) cc_final: -0.4989 (mmt) REVERT: C 377 MET cc_start: 0.6372 (ptm) cc_final: 0.6076 (tmm) REVERT: C 595 MET cc_start: 0.6556 (mtp) cc_final: 0.6177 (mtm) REVERT: C 617 MET cc_start: -0.4654 (mmp) cc_final: -0.5380 (ptp) REVERT: C 697 TYR cc_start: 0.8984 (m-80) cc_final: 0.8631 (m-80) REVERT: C 796 MET cc_start: 0.8762 (mpp) cc_final: 0.8141 (tmm) REVERT: C 905 MET cc_start: 0.9271 (mtm) cc_final: 0.9022 (mtp) REVERT: C 940 MET cc_start: 0.8774 (mmp) cc_final: 0.8512 (mmp) REVERT: C 1130 MET cc_start: 0.9129 (ppp) cc_final: 0.8738 (tmm) REVERT: C 1142 MET cc_start: 0.9175 (mmp) cc_final: 0.8776 (mmp) REVERT: C 1256 MET cc_start: 0.9663 (tpt) cc_final: 0.9088 (tpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1752 time to fit residues: 34.6667 Evaluate side-chains 101 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 224 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** 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 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 131 HIS C 378 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.042303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.028078 restraints weight = 389124.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028723 restraints weight = 281032.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029117 restraints weight = 222762.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029535 restraints weight = 190357.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.029656 restraints weight = 169646.963| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27886 Z= 0.159 Angle : 0.589 10.051 37630 Z= 0.316 Chirality : 0.042 0.159 4133 Planarity : 0.003 0.050 4858 Dihedral : 4.659 34.000 3656 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3379 helix: 1.09 (0.12), residues: 1708 sheet: 0.02 (0.22), residues: 570 loop : -1.71 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 843 TYR 0.024 0.001 TYR C 175 PHE 0.034 0.002 PHE C 171 TRP 0.018 0.001 TRP A 280 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00335 (27879) covalent geometry : angle 0.58789 (37620) SS BOND : bond 0.00491 ( 2) SS BOND : angle 1.27802 ( 4) hydrogen bonds : bond 0.03548 ( 1498) hydrogen bonds : angle 4.41047 ( 4377) metal coordination : bond 0.01078 ( 5) metal coordination : angle 2.87433 ( 6) *********************** 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 114 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.046 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: B 170 MET cc_start: 0.8938 (ppp) cc_final: 0.8610 (ppp) REVERT: B 673 MET cc_start: 0.9058 (ptp) cc_final: 0.8634 (ptp) REVERT: B 1159 MET cc_start: 0.6411 (tpp) cc_final: 0.6210 (tpp) REVERT: C 189 MET cc_start: -0.4078 (mmt) cc_final: -0.5261 (mmt) REVERT: C 377 MET cc_start: 0.6375 (ptm) cc_final: 0.6107 (tmm) REVERT: C 595 MET cc_start: 0.6862 (mtp) cc_final: 0.6512 (mtp) REVERT: C 617 MET cc_start: -0.4821 (mmp) cc_final: -0.5663 (ptp) REVERT: C 796 MET cc_start: 0.8832 (mpp) cc_final: 0.8200 (tmm) REVERT: C 905 MET cc_start: 0.9252 (mtm) cc_final: 0.9018 (mtp) REVERT: C 940 MET cc_start: 0.8833 (mmp) cc_final: 0.8579 (mmp) REVERT: C 1130 MET cc_start: 0.9105 (ppp) cc_final: 0.8779 (ppp) REVERT: C 1142 MET cc_start: 0.9263 (mmp) cc_final: 0.9005 (mmm) REVERT: C 1256 MET cc_start: 0.9658 (tpt) cc_final: 0.9089 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1768 time to fit residues: 34.1977 Evaluate side-chains 99 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 155 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 284 optimal weight: 20.0000 chunk 321 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 477 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.041712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.027628 restraints weight = 393233.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028278 restraints weight = 283244.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.028668 restraints weight = 224000.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.029074 restraints weight = 190773.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029225 restraints weight = 170699.932| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27886 Z= 0.179 Angle : 0.616 11.049 37630 Z= 0.329 Chirality : 0.042 0.184 4133 Planarity : 0.004 0.048 4858 Dihedral : 4.720 34.472 3656 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3379 helix: 1.05 (0.12), residues: 1708 sheet: -0.04 (0.22), residues: 572 loop : -1.72 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 400 TYR 0.023 0.002 TYR C1245 PHE 0.027 0.002 PHE C 171 TRP 0.021 0.002 TRP A 280 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00378 (27879) covalent geometry : angle 0.61412 (37620) SS BOND : bond 0.00550 ( 2) SS BOND : angle 0.95699 ( 4) hydrogen bonds : bond 0.03656 ( 1498) hydrogen bonds : angle 4.48088 ( 4377) metal coordination : bond 0.01115 ( 5) metal coordination : angle 3.86467 ( 6) ********************** 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 115 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.169 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: B 170 MET cc_start: 0.8889 (ppp) cc_final: 0.8592 (ppp) REVERT: B 225 MET cc_start: 0.6549 (ppp) cc_final: 0.6072 (ppp) REVERT: B 637 MET cc_start: 0.8796 (tmm) cc_final: 0.8584 (tmm) REVERT: B 673 MET cc_start: 0.9038 (ptp) cc_final: 0.8560 (ptp) REVERT: B 1159 MET cc_start: 0.6564 (tpp) cc_final: 0.6355 (tpp) REVERT: C 27 TRP cc_start: 0.5236 (m100) cc_final: 0.5010 (m100) REVERT: C 36 GLU cc_start: 0.7076 (pt0) cc_final: 0.6722 (tm-30) REVERT: C 189 MET cc_start: -0.3635 (mmt) cc_final: -0.4994 (mmt) REVERT: C 292 MET cc_start: 0.2710 (mmt) cc_final: 0.2434 (mmt) REVERT: C 377 MET cc_start: 0.6356 (ptm) cc_final: 0.6102 (tmm) REVERT: C 514 MET cc_start: 0.1362 (mtm) cc_final: 0.0860 (mmp) REVERT: C 595 MET cc_start: 0.6908 (mtp) cc_final: 0.6699 (mtp) REVERT: C 617 MET cc_start: -0.4870 (mmp) cc_final: -0.5779 (ptp) REVERT: C 796 MET cc_start: 0.8865 (mpp) cc_final: 0.8263 (tmm) REVERT: C 905 MET cc_start: 0.9243 (mtm) cc_final: 0.9000 (mtp) REVERT: C 940 MET cc_start: 0.8839 (mmp) cc_final: 0.8586 (mmp) REVERT: C 1130 MET cc_start: 0.9151 (ppp) cc_final: 0.8853 (ppp) REVERT: C 1142 MET cc_start: 0.9320 (mmp) cc_final: 0.9045 (mmp) REVERT: C 1256 MET cc_start: 0.9668 (tpt) cc_final: 0.9079 (tpp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1786 time to fit residues: 34.9909 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 : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 308 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 chunk 204 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 485 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 131 HIS C 564 ASN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** 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 = 0.3360 r_free = 0.3360 target = 0.041997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.027776 restraints weight = 388666.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028512 restraints weight = 278098.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.028916 restraints weight = 218859.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.029333 restraints weight = 187355.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.029496 restraints weight = 167147.238| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27886 Z= 0.139 Angle : 0.591 11.577 37630 Z= 0.314 Chirality : 0.042 0.176 4133 Planarity : 0.003 0.048 4858 Dihedral : 4.633 34.099 3656 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 3379 helix: 1.15 (0.12), residues: 1703 sheet: -0.00 (0.22), residues: 579 loop : -1.67 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 843 TYR 0.030 0.001 TYR C 833 PHE 0.022 0.001 PHE C 171 TRP 0.016 0.001 TRP A 280 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00297 (27879) covalent geometry : angle 0.58999 (37620) SS BOND : bond 0.00497 ( 2) SS BOND : angle 1.08472 ( 4) hydrogen bonds : bond 0.03457 ( 1498) hydrogen bonds : angle 4.37964 ( 4377) metal coordination : bond 0.00858 ( 5) metal coordination : angle 2.45618 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4990.55 seconds wall clock time: 87 minutes 26.61 seconds (5246.61 seconds total)