Starting phenix.real_space_refine on Sat Sep 12 23:57:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765.map" model { file = "/net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5o9g_3765/09_2026/5o9g_3765_neut.cif" } resolution = 4.8 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= 0.001 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 325 5.49 5 S 39 5.16 5 Be 1 3.05 5 C 11400 2.51 5 N 3594 2.21 5 O 4319 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19681 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 697 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3304 Classifications: {'DNA': 162} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3335 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "W" Number of atoms: 7017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 7017 Classifications: {'peptide': 855} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 825} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.48, per 1000 atoms: 0.18 Number of scatterers: 19681 At special positions: 0 Unit cell: (131.52, 190.43, 138.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 39 16.00 P 325 15.00 F 3 9.00 O 4319 8.00 N 3594 7.00 C 11400 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 613.3 milliseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 60.7% alpha, 5.0% beta 161 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.132A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.682A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.908A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.518A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.779A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.835A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.612A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.870A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 44 removed outlier: 4.527A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.694A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.252A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.543A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.859A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.562A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.602A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.736A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.739A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.860A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.834A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.669A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.561A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.844A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.505A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 4.202A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'W' and resid 203 through 210 Processing helix chain 'W' and resid 221 through 225 removed outlier: 3.565A pdb=" N HIS W 224 " --> pdb=" O SER W 221 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN W 225 " --> pdb=" O HIS W 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 221 through 225' Processing helix chain 'W' and resid 239 through 257 removed outlier: 3.882A pdb=" N ARG W 257 " --> pdb=" O ASP W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 282 removed outlier: 3.607A pdb=" N GLU W 268 " --> pdb=" O ALA W 264 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 283 through 285 No H-bonds generated for 'chain 'W' and resid 283 through 285' Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.843A pdb=" N VAL W 335 " --> pdb=" O ALA W 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 351 Processing helix chain 'W' and resid 378 through 392 Processing helix chain 'W' and resid 406 through 422 Processing helix chain 'W' and resid 436 through 448 Processing helix chain 'W' and resid 460 through 471 removed outlier: 3.742A pdb=" N PHE W 471 " --> pdb=" O ARG W 467 " (cutoff:3.500A) Processing helix chain 'W' and resid 491 through 498 removed outlier: 3.586A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 499 through 504 Processing helix chain 'W' and resid 515 through 520 removed outlier: 3.790A pdb=" N LEU W 518 " --> pdb=" O ALA W 515 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN W 520 " --> pdb=" O ARG W 517 " (cutoff:3.500A) Processing helix chain 'W' and resid 523 through 530 removed outlier: 3.545A pdb=" N ASN W 530 " --> pdb=" O TYR W 526 " (cutoff:3.500A) Processing helix chain 'W' and resid 548 through 560 removed outlier: 3.999A pdb=" N LEU W 552 " --> pdb=" O ASN W 548 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU W 559 " --> pdb=" O LEU W 555 " (cutoff:3.500A) Processing helix chain 'W' and resid 578 through 591 removed outlier: 4.284A pdb=" N ARG W 588 " --> pdb=" O HIS W 584 " (cutoff:3.500A) Processing helix chain 'W' and resid 598 through 606 removed outlier: 3.915A pdb=" N ASP W 601 " --> pdb=" O LEU W 598 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU W 603 " --> pdb=" O LYS W 600 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS W 604 " --> pdb=" O ASP W 601 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER W 605 " --> pdb=" O VAL W 602 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU W 606 " --> pdb=" O GLU W 603 " (cutoff:3.500A) Processing helix chain 'W' and resid 619 through 628 Processing helix chain 'W' and resid 652 through 658 removed outlier: 3.742A pdb=" N LYS W 656 " --> pdb=" O MET W 652 " (cutoff:3.500A) Processing helix chain 'W' and resid 668 through 673 removed outlier: 3.899A pdb=" N VAL W 672 " --> pdb=" O ALA W 668 " (cutoff:3.500A) Processing helix chain 'W' and resid 683 through 692 Processing helix chain 'W' and resid 694 through 709 removed outlier: 3.667A pdb=" N VAL W 698 " --> pdb=" O SER W 694 " (cutoff:3.500A) Processing helix chain 'W' and resid 720 through 731 removed outlier: 3.779A pdb=" N LEU W 724 " --> pdb=" O MET W 720 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP W 725 " --> pdb=" O VAL W 721 " (cutoff:3.500A) Processing helix chain 'W' and resid 746 through 758 removed outlier: 3.892A pdb=" N ILE W 752 " --> pdb=" O ALA W 748 " (cutoff:3.500A) Processing helix chain 'W' and resid 796 through 803 Processing helix chain 'W' and resid 825 through 836 removed outlier: 3.751A pdb=" N VAL W 829 " --> pdb=" O VAL W 825 " (cutoff:3.500A) Processing helix chain 'W' and resid 1011 through 1026 Processing helix chain 'W' and resid 1031 through 1037 Processing helix chain 'W' and resid 1045 through 1090 removed outlier: 3.515A pdb=" N GLU W1073 " --> pdb=" O LYS W1069 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS W1088 " --> pdb=" O ALA W1084 " (cutoff:3.500A) Processing helix chain 'W' and resid 1103 through 1113 Processing helix chain 'W' and resid 1130 through 1149 Processing helix chain 'W' and resid 1154 through 1158 removed outlier: 3.517A pdb=" N LYS W1157 " --> pdb=" O ASP W1154 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE W1158 " --> pdb=" O PRO W1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1154 through 1158' Processing helix chain 'W' and resid 1176 through 1190 removed outlier: 3.544A pdb=" N ASP W1180 " --> pdb=" O THR W1176 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU W1184 " --> pdb=" O ASP W1180 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE W1185 " --> pdb=" O GLU W1181 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY W1186 " --> pdb=" O LYS W1182 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL W1187 " --> pdb=" O LEU W1183 " (cutoff:3.500A) Processing helix chain 'W' and resid 1194 through 1199 removed outlier: 3.684A pdb=" N ILE W1198 " --> pdb=" O SER W1194 " (cutoff:3.500A) Processing helix chain 'W' and resid 1206 through 1210 removed outlier: 3.683A pdb=" N LYS W1209 " --> pdb=" O ILE W1206 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE W1210 " --> pdb=" O THR W1207 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1206 through 1210' Processing helix chain 'W' and resid 1249 through 1266 removed outlier: 3.591A pdb=" N LEU W1253 " --> pdb=" O GLY W1249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG W1256 " --> pdb=" O HIS W1252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.191A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'W' and resid 179 through 187 removed outlier: 5.460A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 287 through 297 removed outlier: 6.340A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG W 295 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN W 304 " --> pdb=" O ARG W 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'W' and resid 487 through 490 removed outlier: 3.862A pdb=" N LEU W 488 " --> pdb=" O HIS W 428 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR W 490 " --> pdb=" O ILE W 430 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP W 513 " --> pdb=" O VAL W 431 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY W 397 " --> pdb=" O ARG W 537 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU W 539 " --> pdb=" O GLY W 397 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE W 398 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 612 through 616 removed outlier: 6.659A pdb=" N VAL W 786 " --> pdb=" O TYR W 817 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU W 819 " --> pdb=" O VAL W 786 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE W 788 " --> pdb=" O LEU W 819 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER W 821 " --> pdb=" O ILE W 788 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU W 715 " --> pdb=" O VAL W 787 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL W 714 " --> pdb=" O PHE W 767 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN W 739 " --> pdb=" O LEU W 768 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 409 hydrogen bonds 806 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4454 1.33 - 1.45: 5619 1.45 - 1.57: 9913 1.57 - 1.69: 648 1.69 - 1.81: 71 Bond restraints: 20705 Sorted by residual: bond pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.567 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.555 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C3' DA J -55 " pdb=" C2' DA J -55 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" F3 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 20700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 29034 2.36 - 4.72: 288 4.72 - 7.08: 11 7.08 - 9.44: 4 9.44 - 11.80: 1 Bond angle restraints: 29338 Sorted by residual: angle pdb=" C LEU D 99 " pdb=" N PRO D 100 " pdb=" CA PRO D 100 " ideal model delta sigma weight residual 119.84 127.89 -8.05 1.25e+00 6.40e-01 4.15e+01 angle pdb=" N3 DT J 67 " pdb=" C4 DT J 67 " pdb=" O4 DT J 67 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I -59 " pdb=" C4 DT I -59 " pdb=" O4 DT I -59 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 29333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 10356 36.00 - 72.00: 1298 72.00 - 107.99: 18 107.99 - 143.99: 2 143.99 - 179.99: 3 Dihedral angle restraints: 11677 sinusoidal: 6978 harmonic: 4699 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.84 179.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 100.81 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PA ADP W1501 " pdb=" PB ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 52.86 -112.86 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 11674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2181 0.036 - 0.072: 844 0.072 - 0.107: 233 0.107 - 0.143: 31 0.143 - 0.179: 1 Chirality restraints: 3290 Sorted by residual: chirality pdb=" CA PRO D 100 " pdb=" N PRO D 100 " pdb=" C PRO D 100 " pdb=" CB PRO D 100 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" C3' DA J -38 " pdb=" C4' DA J -38 " pdb=" O3' DA J -38 " pdb=" C2' DA J -38 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" C3' DT J -57 " pdb=" C4' DT J -57 " pdb=" O3' DT J -57 " pdb=" C2' DT J -57 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 3287 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 98 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C LEU H 98 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU H 98 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU H 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 98 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LEU D 98 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 98 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 99 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 99 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LEU H 99 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU H 99 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO H 100 " -0.010 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1246 2.74 - 3.28: 18751 3.28 - 3.82: 35233 3.82 - 4.36: 41456 4.36 - 4.90: 61964 Nonbonded interactions: 158650 Sorted by model distance: nonbonded pdb=" OP2 DG J 23 " pdb=" NZ LYS W 519 " model vdw 2.194 3.120 nonbonded pdb=" O ASN W1145 " pdb=" OG SER W1149 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.278 3.040 nonbonded pdb=" OP1 DT I -16 " pdb=" NZ LYS W 497 " model vdw 2.288 3.120 nonbonded pdb=" O LEU W 655 " pdb=" OG SER W 659 " model vdw 2.309 3.040 ... (remaining 158645 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1258 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 : 0.005 0.391 20706 Z= 0.497 Angle : 0.624 11.802 29338 Z= 0.555 Chirality : 0.040 0.179 3290 Planarity : 0.003 0.028 2604 Dihedral : 22.569 179.989 8633 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 0.36 % Allowed : 3.43 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.16), residues: 1578 helix: -2.52 (0.12), residues: 885 sheet: -2.20 (0.56), residues: 79 loop : -3.20 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.008 0.001 TYR A 99 PHE 0.007 0.001 PHE W 379 TRP 0.004 0.000 TRP W 311 HIS 0.002 0.000 HIS W 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.42 (20705) covalent geometry : angle 0.62387 / 0.56 (29338) hydrogen bonds : bond 0.12049 / 8.25 ( 1053) hydrogen bonds : angle 7.48046 / 5.29 ( 2705) Misc. bond : bond 0.39098 / 26.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 245 time to evaluate : 0.563 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 TARDY: cannot create tardy model for: "SER W 635 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.2736 (mt) cc_final: 0.1341 (mt) REVERT: C 68 ASN cc_start: 0.8812 (m-40) cc_final: 0.8425 (m110) REVERT: D 60 ASN cc_start: 0.4534 (t0) cc_final: 0.3384 (m110) REVERT: E 81 ASP cc_start: 0.5207 (t0) cc_final: 0.4606 (m-30) REVERT: W 538 MET cc_start: 0.3072 (tpp) cc_final: 0.1785 (mmm) outliers start: 5 outliers final: 0 residues processed: 249 average time/residue: 0.2017 time to fit residues: 70.4000 Evaluate side-chains 113 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 64 ASN ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 424 GLN W 428 HIS W 622 GLN W 667 ASN W 719 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.099425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082255 restraints weight = 112678.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.084038 restraints weight = 66649.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.085398 restraints weight = 43943.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.086368 restraints weight = 31605.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.087073 restraints weight = 24546.245| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2943 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20706 Z= 0.171 Angle : 0.641 11.425 29338 Z= 0.364 Chirality : 0.042 0.263 3290 Planarity : 0.005 0.114 2604 Dihedral : 28.177 178.670 5335 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 0.21 % Allowed : 1.93 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.18), residues: 1578 helix: -0.94 (0.15), residues: 923 sheet: -1.64 (0.57), residues: 80 loop : -3.05 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG W 671 TYR 0.025 0.002 TYR A 99 PHE 0.015 0.002 PHE W 389 TRP 0.022 0.002 TRP W 793 HIS 0.011 0.001 HIS W1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (20705) covalent geometry : angle 0.64136 / 0.36 (29338) hydrogen bonds : bond 0.05137 / 3.47 ( 1053) hydrogen bonds : angle 4.58869 / 3.32 ( 2705) Misc. bond : bond 0.02876 / 1.92 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.565 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 TARDY: cannot create tardy model for: "SER W 635 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.4513 (t0) cc_final: 0.4101 (m-40) REVERT: E 81 ASP cc_start: 0.4951 (t0) cc_final: 0.4588 (m-30) REVERT: W 270 MET cc_start: 0.0845 (ttm) cc_final: 0.0613 (ttm) REVERT: W 307 TYR cc_start: 0.3303 (m-80) cc_final: 0.3037 (m-80) REVERT: W 457 MET cc_start: 0.1433 (mtp) cc_final: 0.0667 (mtp) REVERT: W 525 LEU cc_start: 0.8494 (mt) cc_final: 0.7944 (tp) REVERT: W 538 MET cc_start: 0.5351 (tpp) cc_final: 0.4248 (mmm) REVERT: W 652 MET cc_start: -0.3412 (ptt) cc_final: -0.3668 (pmm) REVERT: W 681 MET cc_start: 0.4020 (tpt) cc_final: 0.3734 (tpt) REVERT: W 815 MET cc_start: -0.0010 (ptm) cc_final: -0.0891 (tmm) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.1718 time to fit residues: 38.3786 Evaluate side-chains 101 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 144 optimal weight: 0.0970 chunk 102 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN W 779 ASN ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.097002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.082340 restraints weight = 138744.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.083628 restraints weight = 87796.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.084549 restraints weight = 60620.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.085148 restraints weight = 45306.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.085622 restraints weight = 36261.826| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3632 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 20706 Z= 0.241 Angle : 0.794 16.617 29338 Z= 0.431 Chirality : 0.047 0.347 3290 Planarity : 0.007 0.129 2604 Dihedral : 28.609 179.006 5335 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 0.57 % Allowed : 3.50 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.20), residues: 1578 helix: -0.46 (0.16), residues: 942 sheet: -1.76 (0.61), residues: 76 loop : -2.86 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG F 36 TYR 0.049 0.003 TYR A 99 PHE 0.031 0.003 PHE W 379 TRP 0.021 0.002 TRP W 417 HIS 0.017 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.24 (20705) covalent geometry : angle 0.79406 / 0.43 (29338) hydrogen bonds : bond 0.06664 / 4.31 ( 1053) hydrogen bonds : angle 4.40028 / 3.18 ( 2705) Misc. bond : bond 0.03494 / 2.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.589 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: D 59 MET cc_start: 0.3217 (tpt) cc_final: 0.1694 (ttm) REVERT: E 81 ASP cc_start: 0.5176 (t0) cc_final: 0.4746 (m-30) REVERT: W 384 ILE cc_start: 0.1906 (OUTLIER) cc_final: 0.1185 (tp) REVERT: W 815 MET cc_start: 0.0485 (ptm) cc_final: -0.0322 (tmm) outliers start: 8 outliers final: 1 residues processed: 154 average time/residue: 0.1631 time to fit residues: 37.5221 Evaluate side-chains 102 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 337 HIS W 516 HIS W 667 ASN ** W 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.076621 restraints weight = 158516.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.078133 restraints weight = 102320.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079295 restraints weight = 71032.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080054 restraints weight = 52739.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.080738 restraints weight = 41938.801| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 20706 Z= 0.307 Angle : 0.968 15.591 29338 Z= 0.526 Chirality : 0.055 0.442 3290 Planarity : 0.009 0.123 2604 Dihedral : 28.949 173.737 5335 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.12 % Favored : 95.63 % Rotamer: Outliers : 0.36 % Allowed : 3.93 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1578 helix: -0.89 (0.16), residues: 927 sheet: -1.52 (0.66), residues: 61 loop : -2.92 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.002 ARG F 36 TYR 0.055 0.004 TYR D 34 PHE 0.052 0.004 PHE W 509 TRP 0.026 0.003 TRP W 793 HIS 0.020 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.31 (20705) covalent geometry : angle 0.96766 / 0.53 (29338) hydrogen bonds : bond 0.08741 / 5.63 ( 1053) hydrogen bonds : angle 4.88837 / 3.54 ( 2705) Misc. bond : bond 0.00551 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.565 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: W 247 LYS cc_start: 0.8662 (tttt) cc_final: 0.8362 (mtmt) REVERT: W 270 MET cc_start: 0.2709 (ttt) cc_final: 0.2480 (ttt) REVERT: W 441 LEU cc_start: 0.7005 (mt) cc_final: 0.6644 (tt) REVERT: W 525 LEU cc_start: 0.8884 (mp) cc_final: 0.8680 (pp) REVERT: W 692 MET cc_start: 0.6724 (mpp) cc_final: 0.6349 (ptp) REVERT: W 815 MET cc_start: 0.1199 (ptm) cc_final: 0.0155 (tmm) REVERT: W 1107 ARG cc_start: 0.8234 (tmt-80) cc_final: 0.7723 (mtt180) REVERT: W 1108 LEU cc_start: 0.8146 (tp) cc_final: 0.7840 (mm) outliers start: 5 outliers final: 1 residues processed: 156 average time/residue: 0.1714 time to fit residues: 39.2966 Evaluate side-chains 112 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 180 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN W 712 HIS W 810 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079607 restraints weight = 141228.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.080851 restraints weight = 89960.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.081713 restraints weight = 61452.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.082390 restraints weight = 45251.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082765 restraints weight = 35835.623| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20706 Z= 0.151 Angle : 0.647 9.744 29338 Z= 0.363 Chirality : 0.044 0.293 3290 Planarity : 0.005 0.069 2604 Dihedral : 28.926 177.146 5335 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 0.07 % Allowed : 1.79 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1578 helix: -0.08 (0.16), residues: 943 sheet: -1.05 (0.70), residues: 61 loop : -2.70 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 20 TYR 0.033 0.002 TYR H 118 PHE 0.024 0.002 PHE W 414 TRP 0.021 0.002 TRP W 417 HIS 0.009 0.001 HIS W 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (20705) covalent geometry : angle 0.64671 / 0.36 (29338) hydrogen bonds : bond 0.05391 / 3.37 ( 1053) hydrogen bonds : angle 4.16053 / 3.02 ( 2705) Misc. bond : bond 0.00028 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.866 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: C 63 LEU cc_start: 0.6032 (mm) cc_final: 0.5654 (pp) REVERT: E 90 MET cc_start: 0.4231 (tmm) cc_final: 0.3659 (tmm) REVERT: F 84 MET cc_start: -0.1312 (mmp) cc_final: -0.1582 (mmp) REVERT: H 118 TYR cc_start: 0.4865 (t80) cc_final: 0.4592 (t80) REVERT: W 247 LYS cc_start: 0.8697 (tttt) cc_final: 0.8445 (ptpt) REVERT: W 538 MET cc_start: 0.6562 (tpt) cc_final: 0.6155 (mmm) REVERT: W 815 MET cc_start: 0.1411 (ptm) cc_final: 0.0319 (tmm) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1782 time to fit residues: 35.6074 Evaluate side-chains 105 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 15 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.093918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.078323 restraints weight = 144596.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.079601 restraints weight = 91112.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080615 restraints weight = 61587.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.081323 restraints weight = 45009.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.081899 restraints weight = 35143.316| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4301 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20706 Z= 0.140 Angle : 0.628 9.378 29338 Z= 0.354 Chirality : 0.043 0.300 3290 Planarity : 0.005 0.057 2604 Dihedral : 28.839 175.231 5335 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 1.21 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1578 helix: 0.25 (0.17), residues: 933 sheet: -1.04 (0.67), residues: 62 loop : -2.49 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 20 TYR 0.046 0.002 TYR W 469 PHE 0.015 0.002 PHE W 509 TRP 0.023 0.001 TRP W 417 HIS 0.006 0.001 HIS W 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (20705) covalent geometry : angle 0.62804 / 0.35 (29338) hydrogen bonds : bond 0.05147 / 3.26 ( 1053) hydrogen bonds : angle 3.98562 / 2.89 ( 2705) Misc. bond : bond 0.00026 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.498 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: C 93 LEU cc_start: 0.8510 (mt) cc_final: 0.8286 (mt) REVERT: D 105 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8010 (mmtt) REVERT: E 90 MET cc_start: 0.4203 (tmm) cc_final: 0.3939 (tmm) REVERT: F 84 MET cc_start: -0.1247 (mmp) cc_final: -0.1486 (mmp) REVERT: W 538 MET cc_start: 0.6003 (tpt) cc_final: 0.5359 (mmm) REVERT: W 815 MET cc_start: 0.2188 (ptm) cc_final: 0.1281 (tmm) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1652 time to fit residues: 33.9364 Evaluate side-chains 105 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 159 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 536 ASN W 667 ASN W 737 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075294 restraints weight = 158243.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076799 restraints weight = 103198.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077863 restraints weight = 72141.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.078726 restraints weight = 54201.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.079251 restraints weight = 43123.199| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4560 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20706 Z= 0.196 Angle : 0.708 11.106 29338 Z= 0.393 Chirality : 0.045 0.302 3290 Planarity : 0.006 0.121 2604 Dihedral : 28.903 176.790 5335 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 0.14 % Allowed : 1.50 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1578 helix: -0.01 (0.17), residues: 937 sheet: -1.28 (0.65), residues: 62 loop : -2.51 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG E 128 TYR 0.028 0.002 TYR D 34 PHE 0.016 0.002 PHE W 471 TRP 0.017 0.002 TRP W 793 HIS 0.010 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (20705) covalent geometry : angle 0.70760 / 0.39 (29338) hydrogen bonds : bond 0.06339 / 4.08 ( 1053) hydrogen bonds : angle 4.25154 / 3.10 ( 2705) Misc. bond : bond 0.00069 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.576 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: C 93 LEU cc_start: 0.8416 (mt) cc_final: 0.8178 (mt) REVERT: D 103 LEU cc_start: 0.6428 (mt) cc_final: 0.6126 (mt) REVERT: E 90 MET cc_start: 0.4306 (tmm) cc_final: 0.3857 (tmm) REVERT: H 42 LEU cc_start: 0.6572 (tp) cc_final: 0.6360 (tp) REVERT: H 56 MET cc_start: 0.1340 (mpp) cc_final: 0.1031 (mpp) REVERT: W 538 MET cc_start: 0.5769 (tpt) cc_final: 0.5564 (mmm) REVERT: W 548 ASN cc_start: 0.6975 (m110) cc_final: 0.6760 (m110) REVERT: W 617 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6544 (tt0) REVERT: W 697 MET cc_start: 0.2093 (ptt) cc_final: 0.1737 (ptt) REVERT: W 815 MET cc_start: 0.2791 (ptm) cc_final: 0.1804 (tmm) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1659 time to fit residues: 35.7973 Evaluate side-chains 115 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 591 GLN W 667 ASN W 737 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.075676 restraints weight = 156868.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.077237 restraints weight = 101305.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.078310 restraints weight = 71169.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079065 restraints weight = 53191.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079679 restraints weight = 42436.182| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4649 moved from start: 0.9266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 20706 Z= 0.153 Angle : 0.662 11.124 29338 Z= 0.369 Chirality : 0.044 0.309 3290 Planarity : 0.006 0.097 2604 Dihedral : 28.930 178.695 5335 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.21), residues: 1578 helix: 0.25 (0.17), residues: 936 sheet: -1.39 (0.65), residues: 62 loop : -2.35 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 128 TYR 0.028 0.002 TYR D 34 PHE 0.019 0.002 PHE B 61 TRP 0.026 0.001 TRP W1195 HIS 0.022 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20705) covalent geometry : angle 0.66215 / 0.37 (29338) hydrogen bonds : bond 0.04881 / 3.08 ( 1053) hydrogen bonds : angle 3.98212 / 2.90 ( 2705) Misc. bond : bond 0.00076 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.573 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: C 63 LEU cc_start: 0.6508 (mm) cc_final: 0.6042 (pp) REVERT: C 93 LEU cc_start: 0.8448 (mt) cc_final: 0.8200 (mt) REVERT: D 105 LYS cc_start: 0.8413 (mmmt) cc_final: 0.7931 (mmtt) REVERT: D 106 HIS cc_start: 0.6902 (t-90) cc_final: 0.6681 (t-90) REVERT: H 42 LEU cc_start: 0.6658 (tp) cc_final: 0.6380 (tp) REVERT: H 56 MET cc_start: 0.1305 (mpp) cc_final: 0.1037 (mpp) REVERT: H 58 ILE cc_start: 0.3237 (mt) cc_final: 0.2684 (tp) REVERT: W 548 ASN cc_start: 0.7157 (m110) cc_final: 0.6936 (m110) REVERT: W 815 MET cc_start: 0.3837 (ptm) cc_final: 0.3243 (tmm) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.1516 time to fit residues: 33.1835 Evaluate side-chains 120 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 50.0000 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 425 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.075193 restraints weight = 157224.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076743 restraints weight = 101211.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077855 restraints weight = 70265.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.078613 restraints weight = 52477.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.079098 restraints weight = 41742.527| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.9659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20706 Z= 0.151 Angle : 0.641 8.304 29338 Z= 0.361 Chirality : 0.043 0.308 3290 Planarity : 0.005 0.064 2604 Dihedral : 28.879 179.311 5335 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1578 helix: 0.38 (0.17), residues: 937 sheet: -1.49 (0.62), residues: 67 loop : -2.24 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 81 TYR 0.021 0.002 TYR D 34 PHE 0.018 0.002 PHE W 532 TRP 0.020 0.002 TRP W 507 HIS 0.007 0.001 HIS W 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (20705) covalent geometry : angle 0.64080 / 0.36 (29338) hydrogen bonds : bond 0.05136 / 3.29 ( 1053) hydrogen bonds : angle 3.95031 / 2.86 ( 2705) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.582 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: C 63 LEU cc_start: 0.6382 (mm) cc_final: 0.5973 (pp) REVERT: E 79 LYS cc_start: 0.3203 (tptt) cc_final: 0.2843 (mmtm) REVERT: H 42 LEU cc_start: 0.7039 (tp) cc_final: 0.6724 (tp) REVERT: H 56 MET cc_start: 0.3116 (mpp) cc_final: 0.2814 (mpp) REVERT: W 538 MET cc_start: 0.7177 (tpt) cc_final: 0.6043 (mmm) REVERT: W 548 ASN cc_start: 0.7138 (m110) cc_final: 0.6899 (m110) REVERT: W 617 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6498 (tt0) REVERT: W 623 THR cc_start: 0.7960 (m) cc_final: 0.7489 (p) REVERT: W 697 MET cc_start: 0.2310 (ptt) cc_final: 0.1910 (ptt) REVERT: W 815 MET cc_start: 0.4545 (ptm) cc_final: 0.3759 (tmm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1559 time to fit residues: 32.3480 Evaluate side-chains 111 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 60 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 76 GLN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS W 205 ASN ** W 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.086763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.069828 restraints weight = 164382.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071328 restraints weight = 109450.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.072327 restraints weight = 78439.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073031 restraints weight = 60034.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.073602 restraints weight = 48652.602| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 1.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.234 20706 Z= 0.321 Angle : 1.156 32.514 29338 Z= 0.616 Chirality : 0.062 0.368 3290 Planarity : 0.012 0.184 2604 Dihedral : 29.488 178.366 5335 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 37.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.81 % Favored : 90.87 % Rotamer: Outliers : 0.07 % Allowed : 0.93 % Favored : 99.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.78 (0.19), residues: 1578 helix: -1.13 (0.16), residues: 901 sheet: -2.46 (0.62), residues: 56 loop : -2.79 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG F 67 TYR 0.086 0.005 TYR D 34 PHE 0.039 0.005 PHE E 104 TRP 0.118 0.006 TRP W 417 HIS 0.013 0.003 HIS W 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.32 (20705) covalent geometry : angle 1.15552 / 0.62 (29338) hydrogen bonds : bond 0.11468 / 7.58 ( 1053) hydrogen bonds : angle 5.51800 / 3.99 ( 2705) Misc. bond : bond 0.00338 / 0.23 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.634 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: C 93 LEU cc_start: 0.8963 (mt) cc_final: 0.8723 (mt) REVERT: C 94 ASN cc_start: 0.8612 (t0) cc_final: 0.8333 (m-40) REVERT: D 59 MET cc_start: 0.7916 (tpt) cc_final: 0.6760 (tpp) REVERT: D 105 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8310 (mmtt) REVERT: D 117 LYS cc_start: 0.7934 (tttp) cc_final: 0.7721 (tptt) REVERT: F 84 MET cc_start: 0.0261 (mmp) cc_final: -0.1999 (ppp) REVERT: H 42 LEU cc_start: 0.7974 (tp) cc_final: 0.7484 (tp) REVERT: W 387 MET cc_start: 0.8160 (ttt) cc_final: 0.7594 (ttt) REVERT: W 441 LEU cc_start: 0.7683 (mt) cc_final: 0.6961 (tt) REVERT: W 538 MET cc_start: 0.6634 (tpt) cc_final: 0.5773 (tpp) REVERT: W 548 ASN cc_start: 0.7633 (m110) cc_final: 0.7360 (m110) REVERT: W 624 GLU cc_start: 0.8384 (pt0) cc_final: 0.7941 (pp20) REVERT: W 652 MET cc_start: 0.1788 (ppp) cc_final: 0.1325 (ppp) REVERT: W 697 MET cc_start: 0.3821 (ptt) cc_final: 0.1350 (ptt) REVERT: W 815 MET cc_start: 0.5511 (ptm) cc_final: 0.5235 (tmm) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1653 time to fit residues: 44.6484 Evaluate side-chains 128 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 174 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 117 optimal weight: 0.0070 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN ** W 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.088911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.071734 restraints weight = 160654.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073267 restraints weight = 103331.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.074378 restraints weight = 72223.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075192 restraints weight = 54272.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.075705 restraints weight = 43363.802| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 1.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20706 Z= 0.177 Angle : 0.761 10.287 29338 Z= 0.424 Chirality : 0.048 0.320 3290 Planarity : 0.006 0.095 2604 Dihedral : 29.389 177.613 5335 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1578 helix: -0.37 (0.16), residues: 929 sheet: -2.03 (0.63), residues: 59 loop : -2.65 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 40 TYR 0.033 0.003 TYR G 57 PHE 0.027 0.002 PHE W 789 TRP 0.027 0.002 TRP W 507 HIS 0.012 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (20705) covalent geometry : angle 0.76084 / 0.42 (29338) hydrogen bonds : bond 0.05817 / 3.83 ( 1053) hydrogen bonds : angle 4.47651 / 3.24 ( 2705) Misc. bond : bond 0.00163 / 0.11 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3432.41 seconds wall clock time: 60 minutes 4.25 seconds (3604.25 seconds total)