Starting phenix.real_space_refine on Sun Jul 5 11:48:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.map" model { file = "/net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zed_74100/07_2026/9zed_74100.cif" } resolution = 3.94 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 68 5.49 5 S 138 5.16 5 C 16686 2.51 5 N 4551 2.21 5 O 5184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26630 Number of models: 1 Model: "" Number of chains: 14 Chain: "2" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 781 Classifications: {'RNA': 37} Modifications used: {'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p': 8, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "A" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 408 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "A1" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 270 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A2" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1503 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 1 Chain: "A3" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1014 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "B1" Number of atoms: 7142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7142 Classifications: {'peptide': 895} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 849} Chain breaks: 1 Chain: "B2" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1960 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 26, 'TRANS': 223} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B3" Number of atoms: 9396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1198, 9396 Classifications: {'peptide': 1198} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 1136} Chain breaks: 2 Chain: "B4" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1316 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 9, 'TRANS': 158} Chain breaks: 1 Chain: "B5" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "H" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 622 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 11, 'rna3p_pyr': 19} Link IDs: {'rna2p': 11, 'rna3p': 19} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25301 SG CYS H 11 76.201 93.268 54.737 1.00 86.90 S ATOM 25564 SG CYS H 46 74.736 96.232 53.026 1.00 87.89 S ATOM 25587 SG CYS H 49 73.982 92.755 51.676 1.00 93.86 S ATOM 25858 SG CYS H 85 72.356 94.010 54.886 1.00 87.25 S ATOM 25388 SG CYS H 23 59.883 84.272 50.412 1.00 88.14 S ATOM 25412 SG CYS H 26 60.970 84.227 54.066 1.00 87.44 S ATOM 25659 SG CYS H 58 62.850 86.386 51.380 1.00 87.29 S ATOM 25680 SG CYS H 61 62.988 82.484 51.667 1.00 83.55 S ATOM 25439 SG CYS H 30 61.459 89.704 64.261 1.00 83.46 S ATOM 25460 SG CYS H 33 62.131 88.027 67.851 1.00 79.46 S ATOM 25755 SG CYS H 72 59.486 90.770 67.406 1.00 86.12 S ATOM 25779 SG CYS H 75 63.136 91.377 67.076 1.00 86.55 S Time building chain proxies: 4.81, per 1000 atoms: 0.18 Number of scatterers: 26630 At special positions: 0 Unit cell: (145.2, 180.4, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 138 16.00 P 68 15.00 O 5184 8.00 N 4551 7.00 C 16686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 912.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 11 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 85 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 61 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 26 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 23 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 58 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 75 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 33 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 30 " Number of angles added : 18 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 36 sheets defined 41.9% alpha, 18.6% beta 7 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 686 through 701 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.566A pdb=" N GLU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A1' and resid 257 through 274 Processing helix chain 'A2' and resid 20 through 36 Processing helix chain 'A2' and resid 65 through 74 removed outlier: 3.857A pdb=" N GLNA2 74 " --> pdb=" O LEUA2 70 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 93 Processing helix chain 'A3' and resid 393 through 400 removed outlier: 3.622A pdb=" N HISA3 400 " --> pdb=" O LEUA3 396 " (cutoff:3.500A) Processing helix chain 'A3' and resid 418 through 425 Processing helix chain 'A3' and resid 428 through 439 Processing helix chain 'A3' and resid 443 through 447 removed outlier: 3.605A pdb=" N ALAA3 447 " --> pdb=" O ALAA3 444 " (cutoff:3.500A) Processing helix chain 'A3' and resid 451 through 470 Processing helix chain 'A3' and resid 472 through 477 removed outlier: 3.650A pdb=" N GLUA3 477 " --> pdb=" O PROA3 473 " (cutoff:3.500A) Processing helix chain 'A3' and resid 488 through 497 removed outlier: 4.139A pdb=" N ARGA3 497 " --> pdb=" O GLUA3 493 " (cutoff:3.500A) Processing helix chain 'B1' and resid 379 through 396 Processing helix chain 'B1' and resid 400 through 408 Processing helix chain 'B1' and resid 468 through 472 removed outlier: 3.829A pdb=" N ILEB1 472 " --> pdb=" O PROB1 469 " (cutoff:3.500A) Processing helix chain 'B1' and resid 475 through 480 removed outlier: 3.575A pdb=" N LEUB1 479 " --> pdb=" O PHEB1 475 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VALB1 480 " --> pdb=" O ASPB1 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 475 through 480' Processing helix chain 'B1' and resid 488 through 507 Processing helix chain 'B1' and resid 508 through 522 removed outlier: 3.839A pdb=" N ALAB1 514 " --> pdb=" O PROB1 510 " (cutoff:3.500A) Processing helix chain 'B1' and resid 522 through 527 Processing helix chain 'B1' and resid 527 through 540 removed outlier: 3.585A pdb=" N LEUB1 531 " --> pdb=" O GLYB1 527 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLNB1 534 " --> pdb=" O PROB1 530 " (cutoff:3.500A) Proline residue: B1 537 - end of helix removed outlier: 3.709A pdb=" N METB1 540 " --> pdb=" O LEUB1 536 " (cutoff:3.500A) Processing helix chain 'B1' and resid 545 through 563 removed outlier: 3.535A pdb=" N LYSB1 562 " --> pdb=" O ARGB1 558 " (cutoff:3.500A) Processing helix chain 'B1' and resid 570 through 583 removed outlier: 3.896A pdb=" N VALB1 577 " --> pdb=" O LYSB1 573 " (cutoff:3.500A) Proline residue: B1 580 - end of helix removed outlier: 4.372A pdb=" N ILEB1 583 " --> pdb=" O GLUB1 579 " (cutoff:3.500A) Processing helix chain 'B1' and resid 586 through 605 Processing helix chain 'B1' and resid 606 through 614 Processing helix chain 'B1' and resid 615 through 619 removed outlier: 4.025A pdb=" N ASPB1 618 " --> pdb=" O PROB1 615 " (cutoff:3.500A) Processing helix chain 'B1' and resid 621 through 640 Processing helix chain 'B1' and resid 640 through 654 removed outlier: 4.271A pdb=" N LEUB1 644 " --> pdb=" O GLYB1 640 " (cutoff:3.500A) Proline residue: B1 646 - end of helix removed outlier: 3.508A pdb=" N CYSB1 652 " --> pdb=" O LEUB1 648 " (cutoff:3.500A) Processing helix chain 'B1' and resid 657 through 675 removed outlier: 3.882A pdb=" N ARGB1 661 " --> pdb=" O SERB1 657 " (cutoff:3.500A) Processing helix chain 'B1' and resid 676 through 681 removed outlier: 3.907A pdb=" N ILEB1 679 " --> pdb=" O GLYB1 676 " (cutoff:3.500A) Proline residue: B1 681 - end of helix Processing helix chain 'B1' and resid 682 through 692 removed outlier: 3.555A pdb=" N ILEB1 689 " --> pdb=" O SERB1 685 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HISB1 692 " --> pdb=" O GLUB1 688 " (cutoff:3.500A) Processing helix chain 'B1' and resid 693 through 695 No H-bonds generated for 'chain 'B1' and resid 693 through 695' Processing helix chain 'B1' and resid 698 through 716 Processing helix chain 'B1' and resid 724 through 736 removed outlier: 4.211A pdb=" N LYSB1 729 " --> pdb=" O ASPB1 725 " (cutoff:3.500A) Proline residue: B1 730 - end of helix removed outlier: 3.843A pdb=" N LYSB1 733 " --> pdb=" O LYSB1 729 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARGB1 736 " --> pdb=" O TRPB1 732 " (cutoff:3.500A) Processing helix chain 'B1' and resid 740 through 754 Processing helix chain 'B1' and resid 758 through 777 removed outlier: 3.790A pdb=" N ASNB1 763 " --> pdb=" O ALAB1 759 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYRB1 764 " --> pdb=" O GLUB1 760 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLUB1 768 " --> pdb=" O TYRB1 764 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUB1 771 " --> pdb=" O ARGB1 767 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILEB1 772 " --> pdb=" O GLUB1 768 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGB1 775 " --> pdb=" O LEUB1 771 " (cutoff:3.500A) Processing helix chain 'B1' and resid 781 through 798 removed outlier: 3.679A pdb=" N THRB1 798 " --> pdb=" O GLNB1 794 " (cutoff:3.500A) Processing helix chain 'B1' and resid 802 through 810 removed outlier: 4.192A pdb=" N ILEB1 806 " --> pdb=" O GLUB1 802 " (cutoff:3.500A) Processing helix chain 'B1' and resid 810 through 817 removed outlier: 3.923A pdb=" N LYSB1 816 " --> pdb=" O PROB1 812 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HISB1 817 " --> pdb=" O PROB1 813 " (cutoff:3.500A) Processing helix chain 'B1' and resid 820 through 825 removed outlier: 3.640A pdb=" N ALAB1 824 " --> pdb=" O HISB1 821 " (cutoff:3.500A) Processing helix chain 'B1' and resid 826 through 845 removed outlier: 3.592A pdb=" N VALB1 834 " --> pdb=" O TYRB1 830 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYSB1 843 " --> pdb=" O GLUB1 839 " (cutoff:3.500A) Processing helix chain 'B1' and resid 845 through 854 removed outlier: 3.599A pdb=" N ILEB1 849 " --> pdb=" O GLYB1 845 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGB1 852 " --> pdb=" O GLUB1 848 " (cutoff:3.500A) Processing helix chain 'B1' and resid 855 through 859 removed outlier: 3.528A pdb=" N LYSB1 858 " --> pdb=" O ASPB1 855 " (cutoff:3.500A) Processing helix chain 'B1' and resid 861 through 879 Processing helix chain 'B1' and resid 885 through 903 Processing helix chain 'B1' and resid 908 through 922 Processing helix chain 'B1' and resid 923 through 927 removed outlier: 3.789A pdb=" N LYSB1 926 " --> pdb=" O LYSB1 923 " (cutoff:3.500A) Proline residue: B1 927 - end of helix No H-bonds generated for 'chain 'B1' and resid 923 through 927' Processing helix chain 'B1' and resid 928 through 940 Processing helix chain 'B1' and resid 944 through 965 removed outlier: 3.799A pdb=" N ARGB1 948 " --> pdb=" O SERB1 944 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VALB1 960 " --> pdb=" O SERB1 956 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VALB1 961 " --> pdb=" O ARGB1 957 " (cutoff:3.500A) Processing helix chain 'B1' and resid 967 through 981 removed outlier: 3.727A pdb=" N METB1 971 " --> pdb=" O GLUB1 967 " (cutoff:3.500A) Processing helix chain 'B1' and resid 986 through 1005 Processing helix chain 'B1' and resid 1016 through 1024 Proline residue: B11022 - end of helix Processing helix chain 'B1' and resid 1028 through 1047 removed outlier: 3.661A pdb=" N ASNB11034 " --> pdb=" O LYSB11030 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALAB11047 " --> pdb=" O ALAB11043 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1048 through 1050 No H-bonds generated for 'chain 'B1' and resid 1048 through 1050' Processing helix chain 'B1' and resid 1051 through 1066 removed outlier: 3.669A pdb=" N LEUB11063 " --> pdb=" O CYSB11059 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLUB11064 " --> pdb=" O PHEB11060 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUB11066 " --> pdb=" O LEUB11062 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1070 through 1089 removed outlier: 3.647A pdb=" N ARGB11074 " --> pdb=" O LYSB11070 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASNB11079 " --> pdb=" O ARGB11075 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLYB11082 " --> pdb=" O VALB11078 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1090 through 1100 Processing helix chain 'B1' and resid 1106 through 1123 removed outlier: 3.785A pdb=" N THRB11112 " --> pdb=" O ASNB11108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THRB11113 " --> pdb=" O ARGB11109 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1124 through 1127 Processing helix chain 'B1' and resid 1128 through 1136 removed outlier: 3.752A pdb=" N ASNB11134 " --> pdb=" O PROB11130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLUB11135 " --> pdb=" O ALAB11131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYRB11136 " --> pdb=" O LEUB11132 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1140 through 1158 removed outlier: 3.627A pdb=" N LEUB11148 " --> pdb=" O GLNB11144 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1159 through 1164 removed outlier: 3.542A pdb=" N LYSB11163 " --> pdb=" O GLUB11160 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASPB11164 " --> pdb=" O METB11161 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1165 through 1178 Proline residue: B11171 - end of helix Processing helix chain 'B1' and resid 1181 through 1199 removed outlier: 3.698A pdb=" N ARGB11185 " --> pdb=" O ASPB11181 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1204 through 1216 removed outlier: 4.050A pdb=" N LEUB11208 " --> pdb=" O CYSB11204 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASNB11213 " --> pdb=" O ASNB11209 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYRB11214 " --> pdb=" O HISB11210 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1217 through 1221 removed outlier: 4.023A pdb=" N PHEB11220 " --> pdb=" O PROB11217 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLUB11221 " --> pdb=" O ASNB11218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1217 through 1221' Processing helix chain 'B1' and resid 1223 through 1251 removed outlier: 3.586A pdb=" N VALB11239 " --> pdb=" O GLUB11235 " (cutoff:3.500A) Proline residue: B11243 - end of helix removed outlier: 4.054A pdb=" N METB11246 " --> pdb=" O GLYB11242 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1258 through 1276 removed outlier: 3.603A pdb=" N ARGB11262 " --> pdb=" O ALAB11258 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VALB11264 " --> pdb=" O LYSB11260 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1278 through 1284 removed outlier: 3.692A pdb=" N TYRB11284 " --> pdb=" O ILEB11281 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1297 through 1302 removed outlier: 3.528A pdb=" N ASPB11301 " --> pdb=" O ARGB11297 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYRB11302 " --> pdb=" O TYRB11298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1297 through 1302' Processing helix chain 'B2' and resid 452 through 459 removed outlier: 3.741A pdb=" N ASNB2 458 " --> pdb=" O LEUB2 454 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARGB2 459 " --> pdb=" O ARGB2 455 " (cutoff:3.500A) Processing helix chain 'B2' and resid 461 through 467 removed outlier: 3.559A pdb=" N GLNB2 467 " --> pdb=" O ALAB2 463 " (cutoff:3.500A) Processing helix chain 'B2' and resid 477 through 482 removed outlier: 3.909A pdb=" N VALB2 480 " --> pdb=" O METB2 477 " (cutoff:3.500A) Processing helix chain 'B2' and resid 484 through 493 Processing helix chain 'B2' and resid 525 through 531 removed outlier: 4.087A pdb=" N THRB2 531 " --> pdb=" O PHEB2 527 " (cutoff:3.500A) Processing helix chain 'B2' and resid 532 through 547 Processing helix chain 'B2' and resid 551 through 561 removed outlier: 3.731A pdb=" N ARGB2 558 " --> pdb=" O ARGB2 554 " (cutoff:3.500A) Proline residue: B2 559 - end of helix Processing helix chain 'B2' and resid 567 through 575 removed outlier: 3.553A pdb=" N LEUB2 571 " --> pdb=" O ASPB2 567 " (cutoff:3.500A) Processing helix chain 'B2' and resid 594 through 603 removed outlier: 4.080A pdb=" N GLUB2 598 " --> pdb=" O GLYB2 594 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARGB2 600 " --> pdb=" O GLUB2 596 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEUB2 601 " --> pdb=" O PHEB2 597 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLUB2 603 " --> pdb=" O THRB2 599 " (cutoff:3.500A) Processing helix chain 'B2' and resid 610 through 617 removed outlier: 4.108A pdb=" N ARGB2 614 " --> pdb=" O SERB2 610 " (cutoff:3.500A) Processing helix chain 'B2' and resid 624 through 628 removed outlier: 4.140A pdb=" N VALB2 628 " --> pdb=" O ALAB2 625 " (cutoff:3.500A) Processing helix chain 'B2' and resid 632 through 640 Processing helix chain 'B3' and resid 190 through 194 removed outlier: 3.564A pdb=" N ASNB3 194 " --> pdb=" O GLUB3 191 " (cutoff:3.500A) Processing helix chain 'B3' and resid 198 through 203 removed outlier: 3.871A pdb=" N ALAB3 202 " --> pdb=" O GLYB3 198 " (cutoff:3.500A) Processing helix chain 'B3' and resid 429 through 432 Processing helix chain 'B3' and resid 620 through 624 removed outlier: 4.023A pdb=" N CYSB3 624 " --> pdb=" O PROB3 621 " (cutoff:3.500A) Processing helix chain 'B3' and resid 808 through 827 removed outlier: 3.596A pdb=" N ALAB3 827 " --> pdb=" O METB3 823 " (cutoff:3.500A) Processing helix chain 'B3' and resid 832 through 845 Processing helix chain 'B3' and resid 848 through 853 removed outlier: 3.711A pdb=" N GLYB3 853 " --> pdb=" O GLUB3 849 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1072 through 1077 removed outlier: 3.525A pdb=" N LEUB31076 " --> pdb=" O GLYB31072 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRPB31077 " --> pdb=" O ASNB31073 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 1072 through 1077' Processing helix chain 'B3' and resid 1134 through 1152 removed outlier: 3.737A pdb=" N HISB31138 " --> pdb=" O SERB31134 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASPB31139 " --> pdb=" O HISB31135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SERB31150 " --> pdb=" O METB31146 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1159 through 1165 Processing helix chain 'B3' and resid 1175 through 1181 removed outlier: 4.140A pdb=" N CYSB31179 " --> pdb=" O ASPB31175 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1186 through 1197 Processing helix chain 'B3' and resid 1200 through 1214 removed outlier: 3.625A pdb=" N ILEB31211 " --> pdb=" O LYSB31207 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARGB31212 " --> pdb=" O LEUB31208 " (cutoff:3.500A) Processing helix chain 'B4' and resid 25 through 35 removed outlier: 3.931A pdb=" N GLNB4 35 " --> pdb=" O GLUB4 31 " (cutoff:3.500A) Processing helix chain 'B4' and resid 63 through 75 removed outlier: 3.520A pdb=" N ALAB4 67 " --> pdb=" O SERB4 63 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYSB4 72 " --> pdb=" O ASPB4 68 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILEB4 73 " --> pdb=" O TYRB4 69 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASNB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 112 through 121 Processing helix chain 'B4' and resid 151 through 163 Processing helix chain 'B5' and resid 8 through 18 removed outlier: 4.159A pdb=" N GLUB5 12 " --> pdb=" O HISB5 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYSB5 17 " --> pdb=" O HISB5 13 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYRB5 18 " --> pdb=" O LEUB5 14 " (cutoff:3.500A) Processing helix chain 'B5' and resid 27 through 46 Processing helix chain 'B5' and resid 46 through 57 removed outlier: 3.561A pdb=" N LEUB5 50 " --> pdb=" O HISB5 46 " (cutoff:3.500A) Processing helix chain 'B5' and resid 60 through 73 removed outlier: 4.211A pdb=" N LEUB5 73 " --> pdb=" O METB5 69 " (cutoff:3.500A) Processing helix chain 'B6' and resid 5 through 11 Processing helix chain 'B6' and resid 31 through 41 removed outlier: 3.654A pdb=" N LYSB6 41 " --> pdb=" O ASPB6 37 " (cutoff:3.500A) Processing helix chain 'B6' and resid 66 through 78 removed outlier: 3.563A pdb=" N SERB6 78 " --> pdb=" O CYSB6 74 " (cutoff:3.500A) Processing helix chain 'B6' and resid 93 through 98 Processing helix chain 'H' and resid 47 through 55 removed outlier: 3.838A pdb=" N TYR H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY H 52 " --> pdb=" O CYS H 49 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N SER H 53 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 93 through 103 Processing sheet with id=AA1, first strand: chain 'A1' and resid 279 through 284 removed outlier: 6.187A pdb=" N VALA1 280 " --> pdb=" O ALAA2 180 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYSA2 182 " --> pdb=" O VALA1 280 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VALA1 282 " --> pdb=" O LYSA2 182 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N THRA1 284 " --> pdb=" O PROA2 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A2' and resid 46 through 47 removed outlier: 3.537A pdb=" N THRA2 61 " --> pdb=" O CYSA2 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.725A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HISA2 211 " --> pdb=" O ASPA2 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.725A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A3' and resid 406 through 408 Processing sheet with id=AA6, first strand: chain 'A3' and resid 479 through 480 Processing sheet with id=AA7, first strand: chain 'B1' and resid 412 through 414 removed outlier: 3.677A pdb=" N GLNB6 47 " --> pdb=" O VALB6 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B3' and resid 1101 through 1107 removed outlier: 3.981A pdb=" N SERB31103 " --> pdb=" O THRB31120 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILEB31126 " --> pdb=" O LEUB3 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B3' and resid 16 through 20 removed outlier: 3.777A pdb=" N PHEB3 16 " --> pdb=" O SERB3 33 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEUB3 54 " --> pdb=" O LEUB3 40 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARGB3 42 " --> pdb=" O THRB3 52 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THRB3 52 " --> pdb=" O ARGB3 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B3' and resid 62 through 68 removed outlier: 3.505A pdb=" N VALB3 80 " --> pdb=" O VALB3 88 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VALB3 88 " --> pdb=" O VALB3 80 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SERB3 82 " --> pdb=" O ARGB3 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARGB3 86 " --> pdb=" O SERB3 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILEB3 87 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLNB3 104 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILEB3 89 " --> pdb=" O ILEB3 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N METB3 98 " --> pdb=" O GLNB3 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AB3, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AB4, first strand: chain 'B3' and resid 166 through 173 removed outlier: 5.806A pdb=" N VALB3 167 " --> pdb=" O METB3 187 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N METB3 187 " --> pdb=" O VALB3 167 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HISB3 169 " --> pdb=" O LEUB3 185 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N METB3 181 " --> pdb=" O VALB3 173 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYRB3 224 " --> pdb=" O PHEB3 210 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLUB3 212 " --> pdb=" O ARGB3 222 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARGB3 222 " --> pdb=" O GLUB3 212 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASPB3 214 " --> pdb=" O VALB3 220 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VALB3 220 " --> pdb=" O ASPB3 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B3' and resid 232 through 238 removed outlier: 3.881A pdb=" N PHEB3 234 " --> pdb=" O CYSB3 251 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLYB3 247 " --> pdb=" O VALB3 238 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYRB3 255 " --> pdb=" O SERB3 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 273 through 274 removed outlier: 5.857A pdb=" N ARGB3 273 " --> pdb=" O PHEB3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B3' and resid 287 through 294 removed outlier: 3.866A pdb=" N CYSB3 289 " --> pdb=" O GLNB3 304 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHEB3 299 " --> pdb=" O LEUB3 315 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEUB3 315 " --> pdb=" O PHEB3 299 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASPB3 309 " --> pdb=" O THRB3 305 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILEB3 310 " --> pdb=" O TYRB3 329 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYRB3 329 " --> pdb=" O ILEB3 310 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYSB3 312 " --> pdb=" O LEUB3 327 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEUB3 327 " --> pdb=" O LYSB3 312 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THRB3 314 " --> pdb=" O ILEB3 325 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILEB3 325 " --> pdb=" O THRB3 314 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLUB3 316 " --> pdb=" O THRB3 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 340 through 342 removed outlier: 3.680A pdb=" N CYSB3 340 " --> pdb=" O PHEB3 348 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHEB3 348 " --> pdb=" O CYSB3 340 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHEB3 346 " --> pdb=" O LEUB3 342 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEUB3 358 " --> pdb=" O ASPB3 399 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASPB3 399 " --> pdb=" O LEUB3 358 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLNB3 360 " --> pdb=" O LEUB3 397 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEUB3 397 " --> pdb=" O GLNB3 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B3' and resid 409 through 413 removed outlier: 3.750A pdb=" N PHEB3 409 " --> pdb=" O ALAB3 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 445 through 451 removed outlier: 6.852A pdb=" N ILEB3 764 " --> pdb=" O METB3 447 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VALB3 449 " --> pdb=" O LEUB3 762 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEUB3 762 " --> pdb=" O VALB3 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 458 through 462 removed outlier: 4.227A pdb=" N VALB3 484 " --> pdb=" O VALB3 494 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 507 through 509 removed outlier: 3.794A pdb=" N HISB3 526 " --> pdb=" O ASNB3 534 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASNB3 534 " --> pdb=" O HISB3 526 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B3' and resid 544 through 549 Processing sheet with id=AC5, first strand: chain 'B3' and resid 587 through 592 removed outlier: 6.678A pdb=" N GLYB3 608 " --> pdb=" O VALB3 588 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N METB3 590 " --> pdb=" O ALAB3 606 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALAB3 606 " --> pdb=" O METB3 590 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THRB3 613 " --> pdb=" O LEUB3 609 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SERB3 629 " --> pdb=" O ILEB3 616 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SERB3 618 " --> pdb=" O PROB3 627 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B3' and resid 637 through 643 removed outlier: 4.398A pdb=" N SERB3 639 " --> pdb=" O GLYB3 668 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 700 through 706 removed outlier: 3.598A pdb=" N LYSB3 700 " --> pdb=" O METB3 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 784 through 790 removed outlier: 7.410A pdb=" N ILEB3 800 " --> pdb=" O ARGB3 786 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHEB3 788 " --> pdb=" O ILEB3 798 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILEB3 798 " --> pdb=" O PHEB3 788 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SERB3 864 " --> pdb=" O GLNB3 881 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLNB3 881 " --> pdb=" O SERB3 864 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILEB3 866 " --> pdb=" O LEUB3 879 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEUB3 879 " --> pdb=" O ILEB3 866 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VALB3 868 " --> pdb=" O LEUB3 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 886 through 894 removed outlier: 5.751A pdb=" N ALAB3 888 " --> pdb=" O ALAB3 910 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALAB3 910 " --> pdb=" O ALAB3 888 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SERB3 890 " --> pdb=" O GLYB3 908 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRPB3 903 " --> pdb=" O LEUB3 930 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HISB3 941 " --> pdb=" O THRB3 927 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYSB3 929 " --> pdb=" O PHEB3 939 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHEB3 939 " --> pdb=" O LYSB3 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 951 through 955 removed outlier: 3.718A pdb=" N ALAB3 951 " --> pdb=" O GLYB3 962 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEUB3 967 " --> pdb=" O GLUB3 982 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLUB3 982 " --> pdb=" O LEUB3 967 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VALB3 969 " --> pdb=" O LYSB3 980 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 990 through 995 removed outlier: 6.738A pdb=" N SERB31003 " --> pdb=" O SERB3 991 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILEB3 993 " --> pdb=" O ILEB31001 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILEB31001 " --> pdb=" O ILEB3 993 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THRB3 995 " --> pdb=" O ARGB3 999 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ARGB3 999 " --> pdb=" O THRB3 995 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRPB31011 " --> pdb=" O PHEB31024 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 1033 through 1038 removed outlier: 7.114A pdb=" N ALAB31047 " --> pdb=" O THRB31034 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALAB31036 " --> pdb=" O ALAB31045 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALAB31045 " --> pdb=" O ALAB31036 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASPB31048 " --> pdb=" O ASNB31052 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASNB31052 " --> pdb=" O ASPB31048 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILEB31053 " --> pdb=" O ASNB31094 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASNB31094 " --> pdb=" O ILEB31053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VALB31055 " --> pdb=" O ILEB31092 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B4' and resid 39 through 43 removed outlier: 3.704A pdb=" N ASNB4 41 " --> pdb=" O GLUB4 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILEB4 77 " --> pdb=" O ILEB4 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 131 through 134 removed outlier: 7.392A pdb=" N LYSB4 131 " --> pdb=" O TYRB4 144 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYRB4 144 " --> pdb=" O LYSB4 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N METB4 133 " --> pdb=" O LYSB4 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B6' and resid 81 through 82 Processing sheet with id=AD7, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.103A pdb=" N ALA H 18 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 45 " --> pdb=" O ALA H 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.598A pdb=" N SER H 67 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 39 through 42 removed outlier: 6.366A pdb=" N TYR H 71 " --> pdb=" O CYS H 40 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7982 1.34 - 1.46: 4509 1.46 - 1.58: 14480 1.58 - 1.70: 134 1.70 - 1.82: 219 Bond restraints: 27324 Sorted by residual: bond pdb=" N TRPB2 708 " pdb=" CA TRPB2 708 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.31e-02 5.83e+03 7.33e+00 bond pdb=" N GLUB2 710 " pdb=" CA GLUB2 710 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N LEUB2 711 " pdb=" CA LEUB2 711 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.26e+00 bond pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sigma weight residual 1.381 1.399 -0.018 9.00e-03 1.23e+04 4.07e+00 bond pdb=" C LYSB1 926 " pdb=" N PROB1 927 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.45e+00 ... (remaining 27319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 36739 1.68 - 3.36: 442 3.36 - 5.04: 80 5.04 - 6.72: 15 6.72 - 8.40: 7 Bond angle restraints: 37283 Sorted by residual: angle pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sigma weight residual 117.70 122.89 -5.19 1.20e+00 6.94e-01 1.87e+01 angle pdb=" N1 U R 12 " pdb=" C2 U R 12 " pdb=" O2 U R 12 " ideal model delta sigma weight residual 122.80 125.71 -2.91 7.00e-01 2.04e+00 1.73e+01 angle pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C6 U R 12 " ideal model delta sigma weight residual 121.20 115.94 5.26 1.40e+00 5.10e-01 1.41e+01 angle pdb=" C1' U R -12 " pdb=" N1 U R -12 " pdb=" C2 U R -12 " ideal model delta sigma weight residual 117.70 122.17 -4.47 1.20e+00 6.94e-01 1.39e+01 angle pdb=" N1 U R -12 " pdb=" C2 U R -12 " pdb=" O2 U R -12 " ideal model delta sigma weight residual 122.80 125.35 -2.55 7.00e-01 2.04e+00 1.33e+01 ... (remaining 37278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 15970 35.99 - 71.98: 658 71.98 - 107.97: 37 107.97 - 143.96: 1 143.96 - 179.95: 7 Dihedral angle restraints: 16673 sinusoidal: 7459 harmonic: 9214 Sorted by residual: dihedral pdb=" O4' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " pdb=" C2 U R 9 " ideal model delta sinusoidal sigma weight residual -128.00 50.98 -178.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 8 " pdb=" C1' U R 8 " pdb=" N1 U R 8 " pdb=" C2 U R 8 " ideal model delta sinusoidal sigma weight residual -128.00 42.96 -170.96 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' U R 12 " pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sinusoidal sigma weight residual 232.00 71.63 160.37 1 1.70e+01 3.46e-03 6.45e+01 ... (remaining 16670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2850 0.032 - 0.064: 863 0.064 - 0.096: 270 0.096 - 0.128: 165 0.128 - 0.161: 16 Chirality restraints: 4164 Sorted by residual: chirality pdb=" C1' U R 1 " pdb=" O4' U R 1 " pdb=" C2' U R 1 " pdb=" N1 U R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" C1' PSU 2 43 " pdb=" O4' PSU 2 43 " pdb=" C2' PSU 2 43 " pdb=" C5 PSU 2 43 " both_signs ideal model delta sigma weight residual False 2.60 2.45 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA THRB11010 " pdb=" N THRB11010 " pdb=" C THRB11010 " pdb=" CB THRB11010 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 4161 not shown) Planarity restraints: 4607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRB1 508 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PROB1 509 " -0.086 5.00e-02 4.00e+02 pdb=" CA PROB1 509 " 0.026 5.00e-02 4.00e+02 pdb=" CD PROB1 509 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEA3 392 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PROA3 393 " 0.086 5.00e-02 4.00e+02 pdb=" CA PROA3 393 " -0.025 5.00e-02 4.00e+02 pdb=" CD PROA3 393 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALB3 333 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PROB3 334 " -0.085 5.00e-02 4.00e+02 pdb=" CA PROB3 334 " 0.025 5.00e-02 4.00e+02 pdb=" CD PROB3 334 " 0.027 5.00e-02 4.00e+02 ... (remaining 4604 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 10670 2.93 - 3.42: 25766 3.42 - 3.91: 43100 3.91 - 4.41: 47585 4.41 - 4.90: 79219 Nonbonded interactions: 206340 Sorted by model distance: nonbonded pdb=" N2 G 2 33 " pdb=" O2 U R 1 " model vdw 2.433 2.496 nonbonded pdb=" O5' U R 12 " pdb=" O4' U R 12 " model vdw 2.466 2.432 nonbonded pdb=" O5' G 2 31 " pdb=" O4' G 2 31 " model vdw 2.494 2.432 nonbonded pdb=" O ASPB2 567 " pdb=" OD1 ASPB2 567 " model vdw 2.512 3.040 nonbonded pdb=" O5' U 2 46 " pdb=" O4' U 2 46 " model vdw 2.515 2.432 ... (remaining 206335 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 29.510 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.002 0.043 27336 Z= 0.109 Angle : 0.510 9.807 37301 Z= 0.274 Chirality : 0.039 0.161 4164 Planarity : 0.004 0.050 4607 Dihedral : 18.221 179.947 10737 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.11 % Allowed : 21.80 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: 0.23 (0.15), residues: 3131 helix: 1.05 (0.16), residues: 1142 sheet: 0.48 (0.22), residues: 548 loop : -0.67 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGB11109 TYR 0.015 0.001 TYRA1 271 PHE 0.015 0.001 PHEB11126 TRP 0.015 0.001 TRPB1 732 HIS 0.010 0.001 HISB2 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (27324) covalent geometry : angle 0.50030 / 0.27 (37283) hydrogen bonds : bond 0.16196 / 13.23 ( 1117) hydrogen bonds : angle 6.17168 / 5.21 ( 3174) metal coordination : bond 0.00700 / 0.46 ( 12) metal coordination : angle 4.52765 / 8.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 643 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 378 MET cc_start: -0.1506 (ttm) cc_final: -0.2161 (mpp) REVERT: B1 500 LEU cc_start: 0.8778 (mt) cc_final: 0.8440 (pp) REVERT: B1 501 LEU cc_start: 0.8980 (mp) cc_final: 0.8690 (mt) REVERT: B1 511 MET cc_start: 0.8583 (mpp) cc_final: 0.8136 (tmm) REVERT: B1 555 VAL cc_start: 0.9199 (t) cc_final: 0.8930 (p) REVERT: B1 914 PHE cc_start: 0.7806 (t80) cc_final: 0.7585 (t80) REVERT: B1 939 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8094 (ttm-80) REVERT: B1 980 GLU cc_start: 0.5568 (mm-30) cc_final: 0.5191 (mm-30) REVERT: B2 527 PHE cc_start: 0.7679 (p90) cc_final: 0.7067 (p90) REVERT: B2 579 GLN cc_start: 0.7126 (tp-100) cc_final: 0.6145 (tt0) REVERT: B2 586 ILE cc_start: 0.8327 (mp) cc_final: 0.7863 (mt) REVERT: B2 602 LYS cc_start: 0.8779 (tppt) cc_final: 0.8442 (mtpt) REVERT: B2 604 LYS cc_start: 0.7403 (ptpp) cc_final: 0.6765 (pttm) REVERT: B3 236 ILE cc_start: 0.6784 (mm) cc_final: 0.6321 (mt) REVERT: B3 305 THR cc_start: 0.8078 (p) cc_final: 0.7850 (p) REVERT: B3 469 GLU cc_start: 0.6806 (tt0) cc_final: 0.6336 (pm20) REVERT: B3 590 MET cc_start: 0.4779 (mmm) cc_final: 0.4302 (mtp) REVERT: B3 630 MET cc_start: 0.6986 (mmp) cc_final: 0.6596 (tmm) REVERT: B3 730 HIS cc_start: 0.7444 (m-70) cc_final: 0.7226 (m170) REVERT: B3 819 MET cc_start: 0.4254 (mtt) cc_final: 0.4015 (mtt) REVERT: B3 1166 TYR cc_start: 0.8614 (t80) cc_final: 0.8288 (t80) REVERT: B3 1215 TYR cc_start: 0.7410 (m-80) cc_final: 0.7128 (m-10) REVERT: B4 1 MET cc_start: 0.4126 (tmm) cc_final: 0.3876 (tmm) REVERT: B4 40 VAL cc_start: 0.7192 (t) cc_final: 0.6715 (m) REVERT: B4 42 THR cc_start: 0.8714 (p) cc_final: 0.7604 (p) REVERT: B4 74 MET cc_start: 0.7922 (mmt) cc_final: 0.7683 (tpp) REVERT: B4 77 ILE cc_start: 0.8327 (mm) cc_final: 0.7892 (mm) REVERT: B4 106 ASN cc_start: 0.7006 (t0) cc_final: 0.6723 (t0) REVERT: B4 146 PHE cc_start: 0.6172 (m-80) cc_final: 0.5512 (m-80) REVERT: B4 147 ILE cc_start: 0.7698 (mt) cc_final: 0.7404 (tt) REVERT: B4 170 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7267 (mmt180) REVERT: B4 178 PHE cc_start: 0.7774 (m-80) cc_final: 0.7487 (m-80) REVERT: B5 16 SER cc_start: 0.8024 (p) cc_final: 0.7804 (p) REVERT: B6 39 PHE cc_start: 0.7347 (m-80) cc_final: 0.6435 (m-80) REVERT: B6 77 LEU cc_start: 0.4387 (mt) cc_final: 0.4132 (mt) REVERT: B6 86 TYR cc_start: 0.3986 (m-80) cc_final: 0.3636 (m-10) REVERT: H 83 ASP cc_start: 0.5629 (m-30) cc_final: 0.5389 (p0) outliers start: 3 outliers final: 1 residues processed: 646 average time/residue: 0.1911 time to fit residues: 189.1123 Evaluate side-chains 321 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B3 residue 898 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3 423 GLN A3 448 ASN B1 973 HIS B11002 ASN B11209 ASN ** B11277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11293 ASN B2 467 GLN ** B2 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 666 ASN ** B3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 885 ASN B31052 ASN B31061 ASN B5 58 ASN B6 4 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.140721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.117712 restraints weight = 84356.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.118379 restraints weight = 76029.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.119034 restraints weight = 60663.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.119000 restraints weight = 40687.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.119248 restraints weight = 39375.359| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27336 Z= 0.159 Angle : 0.664 11.277 37301 Z= 0.334 Chirality : 0.044 0.225 4164 Planarity : 0.005 0.078 4607 Dihedral : 13.938 179.587 4497 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.90 % Allowed : 23.78 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: 0.15 (0.15), residues: 3131 helix: 1.08 (0.16), residues: 1135 sheet: 0.41 (0.22), residues: 551 loop : -0.78 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGB3 895 TYR 0.027 0.002 TYRB1 981 PHE 0.028 0.002 PHEB11202 TRP 0.038 0.002 TRPB4 30 HIS 0.017 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (27324) covalent geometry : angle 0.65891 / 0.33 (37283) hydrogen bonds : bond 0.04980 / 4.31 ( 1117) hydrogen bonds : angle 5.00345 / 4.25 ( 3174) metal coordination : bond 0.00552 / 0.37 ( 12) metal coordination : angle 3.64155 / 7.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4651 (OUTLIER) cc_final: 0.4165 (ttm) REVERT: B1 555 VAL cc_start: 0.8708 (t) cc_final: 0.8364 (p) REVERT: B1 971 MET cc_start: 0.7724 (mtp) cc_final: 0.7433 (mtp) REVERT: B1 981 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: B1 1015 ASP cc_start: 0.7714 (m-30) cc_final: 0.6408 (t0) REVERT: B2 527 PHE cc_start: 0.7090 (p90) cc_final: 0.6612 (p90) REVERT: B2 586 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7960 (mt) REVERT: B3 298 MET cc_start: 0.7195 (pmm) cc_final: 0.6944 (pmm) REVERT: B3 569 ASP cc_start: 0.2149 (OUTLIER) cc_final: 0.1700 (m-30) REVERT: B3 1026 ASP cc_start: 0.7522 (m-30) cc_final: 0.7260 (m-30) REVERT: B3 1166 TYR cc_start: 0.8488 (t80) cc_final: 0.8212 (t80) REVERT: B4 30 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.5977 (t60) REVERT: B4 170 ARG cc_start: 0.6929 (mtt180) cc_final: 0.6599 (mmt180) REVERT: B4 178 PHE cc_start: 0.7415 (m-80) cc_final: 0.7186 (m-80) REVERT: B6 39 PHE cc_start: 0.6802 (m-80) cc_final: 0.6286 (m-80) REVERT: B6 86 TYR cc_start: 0.4698 (m-80) cc_final: 0.4118 (m-10) REVERT: H 1 MET cc_start: 0.6760 (mtm) cc_final: 0.6466 (tpp) outliers start: 79 outliers final: 24 residues processed: 405 average time/residue: 0.1696 time to fit residues: 108.7748 Evaluate side-chains 310 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 286 ASP Chi-restraints excluded: chain A2 residue 53 SER Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 974 LEU Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1124 SER Chi-restraints excluded: chain B1 residue 1226 VAL Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B3 residue 7 THR Chi-restraints excluded: chain B3 residue 132 ILE Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 705 ARG Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 1109 LEU Chi-restraints excluded: chain B3 residue 1128 ILE Chi-restraints excluded: chain B4 residue 30 TRP Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B6 residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 204 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 293 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 24 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 534 GLN B11225 HIS ** B11277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 587 HIS ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B31061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.139758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.116162 restraints weight = 84078.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.115245 restraints weight = 81515.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.116598 restraints weight = 62028.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.116722 restraints weight = 41694.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.116944 restraints weight = 41865.694| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27336 Z= 0.148 Angle : 0.644 12.528 37301 Z= 0.321 Chirality : 0.043 0.250 4164 Planarity : 0.005 0.055 4607 Dihedral : 13.946 179.790 4495 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.19 % Allowed : 24.07 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: 0.06 (0.15), residues: 3131 helix: 1.01 (0.16), residues: 1148 sheet: 0.36 (0.22), residues: 558 loop : -0.86 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGB1 939 TYR 0.027 0.002 TYR H 36 PHE 0.022 0.002 PHEB11081 TRP 0.033 0.001 TRPB1 732 HIS 0.004 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (27324) covalent geometry : angle 0.63836 / 0.32 (37283) hydrogen bonds : bond 0.04402 / 3.76 ( 1117) hydrogen bonds : angle 4.84126 / 4.11 ( 3174) metal coordination : bond 0.00552 / 0.36 ( 12) metal coordination : angle 3.78435 / 7.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 298 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.4158 (ttm) REVERT: B1 522 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8543 (mmtm) REVERT: B1 687 VAL cc_start: 0.8381 (t) cc_final: 0.8158 (p) REVERT: B1 1015 ASP cc_start: 0.7725 (m-30) cc_final: 0.6387 (t0) REVERT: B1 1179 ASP cc_start: 0.7984 (t0) cc_final: 0.7744 (t0) REVERT: B2 507 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6851 (mtmm) REVERT: B2 527 PHE cc_start: 0.7046 (p90) cc_final: 0.6490 (p90) REVERT: B2 579 GLN cc_start: 0.6719 (tp-100) cc_final: 0.5847 (tt0) REVERT: B2 586 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B3 774 PHE cc_start: 0.7553 (m-80) cc_final: 0.7258 (m-80) REVERT: B3 1026 ASP cc_start: 0.7588 (m-30) cc_final: 0.7327 (m-30) REVERT: B3 1166 TYR cc_start: 0.8489 (t80) cc_final: 0.8129 (t80) REVERT: B4 30 TRP cc_start: 0.6649 (OUTLIER) cc_final: 0.6294 (t60) REVERT: B4 162 MET cc_start: 0.3229 (ptt) cc_final: 0.2366 (tpp) REVERT: B4 170 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6866 (mmt180) REVERT: B4 178 PHE cc_start: 0.7574 (m-80) cc_final: 0.7327 (m-80) REVERT: B6 39 PHE cc_start: 0.6619 (m-80) cc_final: 0.6240 (m-80) REVERT: B6 86 TYR cc_start: 0.4892 (m-80) cc_final: 0.4365 (m-10) outliers start: 87 outliers final: 42 residues processed: 371 average time/residue: 0.1648 time to fit residues: 97.0910 Evaluate side-chains 312 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 53 SER Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 879 LEU Chi-restraints excluded: chain B1 residue 974 LEU Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B3 residue 7 THR Chi-restraints excluded: chain B3 residue 132 ILE Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 705 ARG Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1109 LEU Chi-restraints excluded: chain B3 residue 1118 VAL Chi-restraints excluded: chain B3 residue 1128 ILE Chi-restraints excluded: chain B3 residue 1197 LEU Chi-restraints excluded: chain B4 residue 30 TRP Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 146 PHE Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 19 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 204 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 277 HIS ** A2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11107 GLN B3 9 GLN ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 457 ASN ** B3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B31105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B31160 HIS B5 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.135102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.111746 restraints weight = 83296.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.111960 restraints weight = 93767.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.112561 restraints weight = 81707.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.112745 restraints weight = 52906.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.113204 restraints weight = 48732.303| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 27336 Z= 0.251 Angle : 0.758 13.338 37301 Z= 0.386 Chirality : 0.047 0.211 4164 Planarity : 0.006 0.055 4607 Dihedral : 14.045 178.616 4495 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.10 % Allowed : 23.19 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 3131 helix: 0.66 (0.15), residues: 1131 sheet: -0.10 (0.22), residues: 570 loop : -1.12 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGB3 463 TYR 0.031 0.003 TYR H 36 PHE 0.027 0.003 PHEB4 149 TRP 0.020 0.002 TRPB3 720 HIS 0.013 0.002 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (27324) covalent geometry : angle 0.74863 / 0.39 (37283) hydrogen bonds : bond 0.05078 / 4.36 ( 1117) hydrogen bonds : angle 5.17595 / 4.35 ( 3174) metal coordination : bond 0.01064 / 0.70 ( 12) metal coordination : angle 5.50694 / 10.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 278 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A3 425 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.6991 (p-80) REVERT: A3 443 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7513 (m) REVERT: B1 632 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: B1 1071 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5975 (tptm) REVERT: B1 1179 ASP cc_start: 0.8303 (t0) cc_final: 0.7961 (t0) REVERT: B2 527 PHE cc_start: 0.7254 (p90) cc_final: 0.6932 (p90) REVERT: B2 586 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B3 58 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (p) REVERT: B3 583 MET cc_start: 0.1450 (mtt) cc_final: 0.1235 (ttm) REVERT: B3 803 ASP cc_start: 0.6872 (t0) cc_final: 0.6422 (m-30) REVERT: B3 819 MET cc_start: 0.3559 (mtt) cc_final: 0.2934 (mtt) REVERT: B3 1151 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: B4 12 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8679 (p0) REVERT: B4 170 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6649 (mmt180) REVERT: B6 39 PHE cc_start: 0.6729 (m-80) cc_final: 0.6348 (m-80) REVERT: B6 86 TYR cc_start: 0.5122 (m-80) cc_final: 0.4645 (m-10) outliers start: 139 outliers final: 82 residues processed: 400 average time/residue: 0.1777 time to fit residues: 114.0187 Evaluate side-chains 331 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 241 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 53 SER Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 464 LEU Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 555 VAL Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 687 VAL Chi-restraints excluded: chain B1 residue 717 THR Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 796 CYS Chi-restraints excluded: chain B1 residue 879 LEU Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 974 LEU Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1071 LYS Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1124 SER Chi-restraints excluded: chain B1 residue 1150 SER Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1215 VAL Chi-restraints excluded: chain B1 residue 1226 VAL Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B2 residue 648 LEU Chi-restraints excluded: chain B3 residue 7 THR Chi-restraints excluded: chain B3 residue 18 ILE Chi-restraints excluded: chain B3 residue 58 VAL Chi-restraints excluded: chain B3 residue 107 PHE Chi-restraints excluded: chain B3 residue 132 ILE Chi-restraints excluded: chain B3 residue 133 SER Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 274 ARG Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 325 ILE Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 705 ARG Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 799 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 905 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B3 residue 990 ILE Chi-restraints excluded: chain B3 residue 995 THR Chi-restraints excluded: chain B3 residue 1001 ILE Chi-restraints excluded: chain B3 residue 1005 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1042 ASP Chi-restraints excluded: chain B3 residue 1083 ASN Chi-restraints excluded: chain B3 residue 1097 VAL Chi-restraints excluded: chain B3 residue 1118 VAL Chi-restraints excluded: chain B3 residue 1128 ILE Chi-restraints excluded: chain B3 residue 1151 GLU Chi-restraints excluded: chain B3 residue 1197 LEU Chi-restraints excluded: chain B4 residue 12 ASP Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 146 PHE Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B5 residue 64 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 30 ILE Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 71 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 269 optimal weight: 0.1980 chunk 273 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 211 HIS A3 423 GLN B1 547 GLN B11209 ASN ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 356 HIS ** B3 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS H 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.138031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.115459 restraints weight = 83578.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.115082 restraints weight = 91528.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.116146 restraints weight = 75111.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.116218 restraints weight = 50464.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.116578 restraints weight = 48742.456| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27336 Z= 0.127 Angle : 0.662 17.556 37301 Z= 0.325 Chirality : 0.043 0.258 4164 Planarity : 0.005 0.129 4607 Dihedral : 13.987 179.953 4495 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.41 % Allowed : 24.59 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.20 (0.15), residues: 3131 helix: 0.90 (0.16), residues: 1141 sheet: 0.08 (0.22), residues: 561 loop : -1.03 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGB3 815 TYR 0.023 0.001 TYRB11136 PHE 0.030 0.001 PHEB4 149 TRP 0.045 0.002 TRPB1 732 HIS 0.011 0.001 HISB3 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (27324) covalent geometry : angle 0.64924 / 0.32 (37283) hydrogen bonds : bond 0.03949 / 3.34 ( 1117) hydrogen bonds : angle 4.79651 / 4.09 ( 3174) metal coordination : bond 0.01511 / 1.01 ( 12) metal coordination : angle 6.02083 / 11.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 270 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 122 GLN cc_start: 0.2753 (OUTLIER) cc_final: 0.2276 (tm-30) REVERT: A2 171 MET cc_start: 0.4726 (OUTLIER) cc_final: 0.4067 (ttm) REVERT: B1 578 ILE cc_start: 0.8330 (mm) cc_final: 0.7921 (tp) REVERT: B1 632 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: B1 903 GLN cc_start: 0.5135 (OUTLIER) cc_final: 0.4710 (pp30) REVERT: B1 1179 ASP cc_start: 0.8090 (t0) cc_final: 0.7754 (t0) REVERT: B1 1231 MET cc_start: 0.7726 (mmm) cc_final: 0.7526 (mmt) REVERT: B2 527 PHE cc_start: 0.6965 (p90) cc_final: 0.6332 (p90) REVERT: B2 586 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8128 (mt) REVERT: B3 181 MET cc_start: 0.6495 (mtt) cc_final: 0.6251 (mtt) REVERT: B3 298 MET cc_start: 0.6601 (pmm) cc_final: 0.6004 (pmm) REVERT: B3 774 PHE cc_start: 0.7641 (m-80) cc_final: 0.7313 (m-80) REVERT: B3 819 MET cc_start: 0.2948 (mtt) cc_final: 0.2681 (mtt) REVERT: B4 1 MET cc_start: 0.5589 (tmm) cc_final: 0.5316 (tmm) REVERT: B4 146 PHE cc_start: 0.3647 (OUTLIER) cc_final: 0.3047 (m-80) REVERT: B4 162 MET cc_start: 0.5028 (mpp) cc_final: 0.3473 (ttt) REVERT: B4 170 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6654 (mmt180) REVERT: B6 39 PHE cc_start: 0.6501 (m-80) cc_final: 0.6170 (m-80) REVERT: B6 86 TYR cc_start: 0.5057 (m-80) cc_final: 0.4472 (m-10) outliers start: 93 outliers final: 51 residues processed: 349 average time/residue: 0.1795 time to fit residues: 100.8945 Evaluate side-chains 301 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 122 GLN Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 464 LEU Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 683 LEU Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 735 ILE Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 500 VAL Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B2 residue 648 LEU Chi-restraints excluded: chain B3 residue 7 THR Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 132 ILE Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 705 ARG Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B4 residue 30 TRP Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 63 SER Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 146 PHE Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 1 optimal weight: 20.0000 chunk 291 optimal weight: 0.9980 chunk 191 optimal weight: 0.0770 chunk 145 optimal weight: 8.9990 chunk 67 optimal weight: 0.0170 chunk 173 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B11209 ASN B2 579 GLN ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 394 ASN ** B3 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 870 ASN B4 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.138524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.115663 restraints weight = 83681.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.114880 restraints weight = 95050.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.116374 restraints weight = 77799.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.116116 restraints weight = 54026.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.116675 restraints weight = 51213.326| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27336 Z= 0.117 Angle : 0.625 13.144 37301 Z= 0.309 Chirality : 0.042 0.168 4164 Planarity : 0.004 0.051 4607 Dihedral : 13.890 179.038 4495 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.83 % Allowed : 25.54 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.07 (0.15), residues: 3131 helix: 1.05 (0.16), residues: 1129 sheet: 0.23 (0.22), residues: 549 loop : -1.01 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 979 TYR 0.023 0.001 TYRB11136 PHE 0.021 0.001 PHEB3 234 TRP 0.019 0.001 TRPB1 732 HIS 0.009 0.001 HISB3 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (27324) covalent geometry : angle 0.61588 / 0.31 (37283) hydrogen bonds : bond 0.03624 / 3.03 ( 1117) hydrogen bonds : angle 4.62543 / 3.97 ( 3174) metal coordination : bond 0.00715 / 0.47 ( 12) metal coordination : angle 4.79831 / 9.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 263 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.3991 (ttm) REVERT: B1 578 ILE cc_start: 0.8335 (mm) cc_final: 0.7916 (tp) REVERT: B1 1179 ASP cc_start: 0.7959 (t0) cc_final: 0.7585 (t0) REVERT: B2 527 PHE cc_start: 0.6911 (p90) cc_final: 0.6361 (p90) REVERT: B2 586 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B3 583 MET cc_start: 0.2266 (ttm) cc_final: 0.1811 (ttt) REVERT: B3 774 PHE cc_start: 0.7555 (m-80) cc_final: 0.7179 (m-80) REVERT: B3 1026 ASP cc_start: 0.7647 (m-30) cc_final: 0.7225 (m-30) REVERT: B4 146 PHE cc_start: 0.3289 (OUTLIER) cc_final: 0.2844 (m-80) REVERT: B4 162 MET cc_start: 0.5461 (mpp) cc_final: 0.3711 (ttt) REVERT: B4 170 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6654 (mmt180) REVERT: B6 22 TYR cc_start: 0.4422 (t80) cc_final: 0.4137 (t80) REVERT: B6 39 PHE cc_start: 0.6484 (m-80) cc_final: 0.6140 (m-80) REVERT: B6 86 TYR cc_start: 0.5486 (m-80) cc_final: 0.5114 (m-10) outliers start: 77 outliers final: 51 residues processed: 323 average time/residue: 0.1800 time to fit residues: 93.7825 Evaluate side-chains 298 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 464 LEU Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 1006 MET Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B2 residue 648 LEU Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 286 ILE Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 843 LEU Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B4 residue 6 ILE Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 146 PHE Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 298 optimal weight: 0.0010 chunk 220 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 197 optimal weight: 0.0570 chunk 241 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B11209 ASN ** B11277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.136433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.109517 restraints weight = 83476.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.108828 restraints weight = 69933.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.109507 restraints weight = 51426.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.109896 restraints weight = 39530.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.110038 restraints weight = 34885.248| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27336 Z= 0.116 Angle : 0.627 13.696 37301 Z= 0.309 Chirality : 0.043 0.294 4164 Planarity : 0.004 0.049 4607 Dihedral : 13.827 179.239 4495 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.90 % Allowed : 25.25 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.07 (0.15), residues: 3131 helix: 1.06 (0.16), residues: 1127 sheet: 0.26 (0.22), residues: 539 loop : -1.02 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 999 TYR 0.023 0.001 TYRB11136 PHE 0.041 0.001 PHEB3 745 TRP 0.020 0.001 TRPB2 632 HIS 0.006 0.001 HISB3 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (27324) covalent geometry : angle 0.61977 / 0.31 (37283) hydrogen bonds : bond 0.03617 / 3.03 ( 1117) hydrogen bonds : angle 4.60327 / 3.95 ( 3174) metal coordination : bond 0.00597 / 0.40 ( 12) metal coordination : angle 4.38127 / 8.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.3776 (ttm) REVERT: B1 578 ILE cc_start: 0.8443 (mm) cc_final: 0.8005 (tp) REVERT: B1 903 GLN cc_start: 0.5317 (OUTLIER) cc_final: 0.4846 (pp30) REVERT: B1 1056 MET cc_start: 0.7875 (ppp) cc_final: 0.7598 (mmm) REVERT: B1 1179 ASP cc_start: 0.7995 (t0) cc_final: 0.7699 (t0) REVERT: B2 527 PHE cc_start: 0.7000 (p90) cc_final: 0.6449 (p90) REVERT: B2 586 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B3 298 MET cc_start: 0.7095 (pmm) cc_final: 0.6339 (pmm) REVERT: B3 774 PHE cc_start: 0.7645 (m-80) cc_final: 0.7272 (m-80) REVERT: B3 1026 ASP cc_start: 0.7704 (m-30) cc_final: 0.7198 (m-30) REVERT: B4 1 MET cc_start: 0.5283 (tmm) cc_final: 0.4995 (tmm) REVERT: B4 146 PHE cc_start: 0.3661 (OUTLIER) cc_final: 0.3156 (m-80) REVERT: B4 162 MET cc_start: 0.5667 (mpp) cc_final: 0.3815 (ttt) REVERT: B4 170 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6815 (mmt180) REVERT: B6 39 PHE cc_start: 0.6771 (m-80) cc_final: 0.6403 (m-80) REVERT: B6 86 TYR cc_start: 0.5603 (m-80) cc_final: 0.5249 (m-10) outliers start: 79 outliers final: 56 residues processed: 322 average time/residue: 0.1758 time to fit residues: 92.1264 Evaluate side-chains 301 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 717 THR Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 771 LEU Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 943 LYS Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 500 VAL Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B2 residue 648 LEU Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 274 ARG Chi-restraints excluded: chain B3 residue 286 ILE Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 372 GLU Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 563 LEU Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 843 LEU Chi-restraints excluded: chain B3 residue 1001 ILE Chi-restraints excluded: chain B3 residue 1128 ILE Chi-restraints excluded: chain B4 residue 6 ILE Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 146 PHE Chi-restraints excluded: chain B4 residue 160 GLU Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 316 optimal weight: 20.0000 chunk 279 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B11209 ASN B2 483 GLN B2 579 GLN ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 873 GLN B5 51 ASN H 4 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.108723 restraints weight = 84069.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.106669 restraints weight = 97978.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.107976 restraints weight = 82312.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.108049 restraints weight = 59550.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.108354 restraints weight = 50415.553| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 27336 Z= 0.219 Angle : 0.722 17.479 37301 Z= 0.363 Chirality : 0.046 0.230 4164 Planarity : 0.005 0.056 4607 Dihedral : 13.852 179.568 4495 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.74 % Allowed : 25.03 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.37 (0.15), residues: 3131 helix: 0.79 (0.16), residues: 1133 sheet: -0.04 (0.23), residues: 533 loop : -1.14 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGB3 832 TYR 0.032 0.002 TYRB3 357 PHE 0.025 0.002 PHEB3 107 TRP 0.019 0.002 TRPB2 632 HIS 0.010 0.002 HISB31160 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (27324) covalent geometry : angle 0.71152 / 0.36 (37283) hydrogen bonds : bond 0.04505 / 3.84 ( 1117) hydrogen bonds : angle 4.96293 / 4.20 ( 3174) metal coordination : bond 0.00893 / 0.58 ( 12) metal coordination : angle 5.60230 / 10.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 247 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.3943 (ttm) REVERT: A3 425 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7099 (p-80) REVERT: B1 632 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: B1 1179 ASP cc_start: 0.8352 (t0) cc_final: 0.8066 (t0) REVERT: B2 527 PHE cc_start: 0.7152 (p90) cc_final: 0.6778 (p90) REVERT: B2 585 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7410 (p) REVERT: B2 586 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B2 604 LYS cc_start: 0.7320 (pptt) cc_final: 0.7038 (pptt) REVERT: B3 583 MET cc_start: 0.2159 (ttm) cc_final: 0.1755 (ttt) REVERT: B3 630 MET cc_start: 0.5977 (tmm) cc_final: 0.5306 (tmm) REVERT: B3 769 LYS cc_start: 0.7461 (mttp) cc_final: 0.7244 (mttp) REVERT: B3 803 ASP cc_start: 0.6792 (t0) cc_final: 0.6507 (m-30) REVERT: B3 1212 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7506 (ttt-90) REVERT: B4 1 MET cc_start: 0.5435 (tmm) cc_final: 0.5129 (tmm) REVERT: B4 76 MET cc_start: 0.7587 (pmm) cc_final: 0.7223 (pmm) REVERT: B6 86 TYR cc_start: 0.5361 (m-80) cc_final: 0.4999 (m-10) outliers start: 102 outliers final: 73 residues processed: 333 average time/residue: 0.1823 time to fit residues: 97.3216 Evaluate side-chains 308 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 464 LEU Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 717 THR Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 735 ILE Chi-restraints excluded: chain B1 residue 771 LEU Chi-restraints excluded: chain B1 residue 943 LYS Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 974 LEU Chi-restraints excluded: chain B1 residue 1006 MET Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1050 VAL Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1150 SER Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 461 THR Chi-restraints excluded: chain B2 residue 500 VAL Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 274 ARG Chi-restraints excluded: chain B3 residue 286 ILE Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 372 GLU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 470 PHE Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 691 THR Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 799 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 843 LEU Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B3 residue 1001 ILE Chi-restraints excluded: chain B3 residue 1005 VAL Chi-restraints excluded: chain B3 residue 1097 VAL Chi-restraints excluded: chain B3 residue 1118 VAL Chi-restraints excluded: chain B3 residue 1128 ILE Chi-restraints excluded: chain B3 residue 1212 ARG Chi-restraints excluded: chain B4 residue 6 ILE Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 160 GLU Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 160 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 201 optimal weight: 30.0000 chunk 172 optimal weight: 0.5980 chunk 259 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B2 490 HIS ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 41 ASN B5 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.135755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.112683 restraints weight = 84323.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.112655 restraints weight = 90860.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.113611 restraints weight = 77801.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.113517 restraints weight = 53819.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.113951 restraints weight = 49900.845| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27336 Z= 0.132 Angle : 0.669 14.300 37301 Z= 0.329 Chirality : 0.043 0.230 4164 Planarity : 0.004 0.051 4607 Dihedral : 13.809 179.642 4495 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.75 % Allowed : 26.13 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.28 (0.15), residues: 3131 helix: 0.87 (0.16), residues: 1120 sheet: 0.02 (0.22), residues: 549 loop : -1.09 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGB1 517 TYR 0.036 0.001 TYRB11136 PHE 0.022 0.001 PHEB3 745 TRP 0.016 0.001 TRPB2 632 HIS 0.007 0.001 HISB3 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (27324) covalent geometry : angle 0.65948 / 0.33 (37283) hydrogen bonds : bond 0.03881 / 3.28 ( 1117) hydrogen bonds : angle 4.79137 / 4.08 ( 3174) metal coordination : bond 0.00719 / 0.48 ( 12) metal coordination : angle 5.15217 / 10.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 242 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.3897 (ttm) REVERT: A3 454 ASP cc_start: 0.8236 (t0) cc_final: 0.8031 (t0) REVERT: B1 561 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: B1 578 ILE cc_start: 0.8344 (mm) cc_final: 0.8061 (tp) REVERT: B1 876 MET cc_start: 0.7661 (ptt) cc_final: 0.7337 (ptp) REVERT: B1 1179 ASP cc_start: 0.8248 (t0) cc_final: 0.7859 (t0) REVERT: B1 1231 MET cc_start: 0.7999 (mmm) cc_final: 0.7531 (mmt) REVERT: B2 527 PHE cc_start: 0.7044 (p90) cc_final: 0.6521 (p90) REVERT: B2 586 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B3 583 MET cc_start: 0.2108 (ttm) cc_final: 0.1772 (ttt) REVERT: B3 630 MET cc_start: 0.6030 (tmm) cc_final: 0.5493 (tmm) REVERT: B4 76 MET cc_start: 0.7428 (pmm) cc_final: 0.7106 (pmm) REVERT: B5 72 MET cc_start: 0.7058 (mmm) cc_final: 0.6513 (tmm) REVERT: B6 86 TYR cc_start: 0.5213 (m-80) cc_final: 0.4880 (m-10) REVERT: H 74 GLU cc_start: 0.6697 (mp0) cc_final: 0.6186 (mp0) outliers start: 75 outliers final: 58 residues processed: 304 average time/residue: 0.1711 time to fit residues: 84.2867 Evaluate side-chains 293 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 561 TYR Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 668 VAL Chi-restraints excluded: chain B1 residue 675 MET Chi-restraints excluded: chain B1 residue 717 THR Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1050 VAL Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 500 VAL Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B3 residue 133 SER Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 274 ARG Chi-restraints excluded: chain B3 residue 286 ILE Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 372 GLU Chi-restraints excluded: chain B3 residue 470 PHE Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 799 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 843 LEU Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B3 residue 1001 ILE Chi-restraints excluded: chain B3 residue 1197 LEU Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 41 ASN Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 160 GLU Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B5 residue 51 ASN Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 34 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 306 optimal weight: 0.0980 chunk 239 optimal weight: 1.9990 chunk 238 optimal weight: 0.0040 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.113196 restraints weight = 84284.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.112650 restraints weight = 92313.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.113822 restraints weight = 76874.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.113637 restraints weight = 52256.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.114118 restraints weight = 50036.793| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27336 Z= 0.126 Angle : 0.661 13.334 37301 Z= 0.325 Chirality : 0.043 0.234 4164 Planarity : 0.005 0.088 4607 Dihedral : 13.758 179.574 4495 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.42 % Allowed : 26.57 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.26 (0.15), residues: 3131 helix: 0.83 (0.16), residues: 1129 sheet: 0.19 (0.22), residues: 538 loop : -1.09 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARGB31212 TYR 0.034 0.001 TYRB11136 PHE 0.020 0.001 PHEB3 745 TRP 0.016 0.001 TRPB2 632 HIS 0.007 0.001 HISB3 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (27324) covalent geometry : angle 0.65219 / 0.32 (37283) hydrogen bonds : bond 0.03757 / 3.18 ( 1117) hydrogen bonds : angle 4.75213 / 4.05 ( 3174) metal coordination : bond 0.00669 / 0.44 ( 12) metal coordination : angle 4.95125 / 9.72 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6262 Ramachandran restraints generated. 3131 Oldfield, 0 Emsley, 3131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 235 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 171 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.3885 (ttm) REVERT: B1 578 ILE cc_start: 0.8319 (mm) cc_final: 0.7900 (tp) REVERT: B1 876 MET cc_start: 0.7654 (ptt) cc_final: 0.7361 (ptp) REVERT: B1 910 MET cc_start: 0.3770 (ppp) cc_final: 0.3540 (ppp) REVERT: B1 1179 ASP cc_start: 0.8205 (t0) cc_final: 0.7806 (t0) REVERT: B1 1231 MET cc_start: 0.7951 (mmm) cc_final: 0.7485 (mmt) REVERT: B2 527 PHE cc_start: 0.7103 (p90) cc_final: 0.6495 (p90) REVERT: B2 586 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B3 583 MET cc_start: 0.2185 (ttm) cc_final: 0.1749 (ttt) REVERT: B3 590 MET cc_start: 0.1167 (mpp) cc_final: 0.0185 (mtt) REVERT: B3 630 MET cc_start: 0.5996 (tmm) cc_final: 0.5513 (tmm) REVERT: B3 803 ASP cc_start: 0.6406 (t0) cc_final: 0.6149 (m-30) REVERT: B4 1 MET cc_start: 0.5358 (tmm) cc_final: 0.3834 (ttp) REVERT: B4 76 MET cc_start: 0.7433 (pmm) cc_final: 0.7075 (pmm) REVERT: B4 170 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6644 (mmt180) REVERT: B6 86 TYR cc_start: 0.5125 (m-80) cc_final: 0.4823 (m-10) REVERT: H 74 GLU cc_start: 0.6683 (mp0) cc_final: 0.6214 (mp0) outliers start: 66 outliers final: 60 residues processed: 286 average time/residue: 0.1749 time to fit residues: 81.8103 Evaluate side-chains 294 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 119 VAL Chi-restraints excluded: chain A2 residue 171 MET Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain B1 residue 467 LEU Chi-restraints excluded: chain B1 residue 486 THR Chi-restraints excluded: chain B1 residue 500 LEU Chi-restraints excluded: chain B1 residue 608 THR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 717 THR Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 1006 MET Chi-restraints excluded: chain B1 residue 1020 LEU Chi-restraints excluded: chain B1 residue 1050 VAL Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1080 THR Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 500 VAL Chi-restraints excluded: chain B2 residue 507 LYS Chi-restraints excluded: chain B2 residue 572 HIS Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 613 LEU Chi-restraints excluded: chain B3 residue 133 SER Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 274 ARG Chi-restraints excluded: chain B3 residue 286 ILE Chi-restraints excluded: chain B3 residue 302 LEU Chi-restraints excluded: chain B3 residue 372 GLU Chi-restraints excluded: chain B3 residue 470 PHE Chi-restraints excluded: chain B3 residue 476 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 619 LEU Chi-restraints excluded: chain B3 residue 691 THR Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 799 ILE Chi-restraints excluded: chain B3 residue 812 LYS Chi-restraints excluded: chain B3 residue 843 LEU Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 1001 ILE Chi-restraints excluded: chain B3 residue 1005 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1197 LEU Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 64 GLU Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 160 GLU Chi-restraints excluded: chain B4 residue 174 VAL Chi-restraints excluded: chain B6 residue 26 LEU Chi-restraints excluded: chain B6 residue 64 TYR Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 122 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 260 optimal weight: 0.5980 chunk 22 optimal weight: 50.0000 chunk 313 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 302 optimal weight: 20.0000 chunk 248 optimal weight: 0.3980 chunk 308 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.113511 restraints weight = 84248.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.113183 restraints weight = 91731.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.114385 restraints weight = 78554.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.114311 restraints weight = 51619.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.115192 restraints weight = 47756.942| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27336 Z= 0.119 Angle : 0.642 12.238 37301 Z= 0.317 Chirality : 0.043 0.226 4164 Planarity : 0.004 0.049 4607 Dihedral : 13.638 179.880 4495 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.42 % Allowed : 26.61 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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 are not related in a simple way. whole: -0.19 (0.15), residues: 3131 helix: 0.92 (0.16), residues: 1126 sheet: 0.23 (0.22), residues: 538 loop : -1.08 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGB31212 TYR 0.034 0.001 TYRA1 271 PHE 0.022 0.001 PHEB4 120 TRP 0.019 0.001 TRPB2 632 HIS 0.007 0.001 HISB3 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27324) covalent geometry : angle 0.63420 / 0.32 (37283) hydrogen bonds : bond 0.03584 / 3.01 ( 1117) hydrogen bonds : angle 4.64230 / 3.99 ( 3174) metal coordination : bond 0.00637 / 0.42 ( 12) metal coordination : angle 4.69209 / 9.20 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.71 seconds wall clock time: 72 minutes 45.57 seconds (4365.57 seconds total)