Starting phenix.real_space_refine on Sat Sep 28 13:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_3765_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_3765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_3765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_3765_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o9g_3765/09_2024/5o9g_3765_neut.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.42, per 1000 atoms: 0.53 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: 4.47 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 7.60 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: 12.34 Time building geometry restraints manager: 5.28 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=" 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 bond pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 1.520 1.554 -0.035 1.42e-02 4.96e+03 5.94e+00 bond pdb=" CA LEU H 99 " pdb=" C LEU H 99 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.06e-02 8.90e+03 5.32e+00 ... (remaining 20700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 29210 2.36 - 4.72: 113 4.72 - 7.08: 10 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=" N VAL D 45 " pdb=" CA VAL D 45 " pdb=" C VAL D 45 " ideal model delta sigma weight residual 113.71 109.63 4.08 9.50e-01 1.11e+00 1.84e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 108.32 11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N PRO D 100 " pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 112.47 120.37 -7.90 2.06e+00 2.36e-01 1.47e+01 angle pdb=" N LEU D 99 " pdb=" CA LEU D 99 " pdb=" C LEU D 99 " ideal model delta sigma weight residual 110.24 114.74 -4.50 1.46e+00 4.69e-01 9.51e+00 ... (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: 2643 0.036 - 0.072: 521 0.072 - 0.107: 103 0.107 - 0.143: 22 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=" CA PRO H 100 " pdb=" N PRO H 100 " pdb=" C PRO H 100 " pdb=" CB PRO H 100 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE W 290 " pdb=" N ILE W 290 " pdb=" C ILE W 290 " pdb=" CB ILE W 290 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-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: 0.860 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 50.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20705 Z= 0.144 Angle : 0.475 11.802 29338 Z= 0.293 Chirality : 0.032 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.000 TRP W 311 HIS 0.002 0.000 HIS W 285 PHE 0.007 0.001 PHE W 379 TYR 0.008 0.001 TYR A 99 ARG 0.002 0.000 ARG B 39 *********************** 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 fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.548 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: 0.2735 (mt) cc_final: 0.1340 (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: 0.3383 (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: 0.1786 (mmm) outliers start: 5 outliers final: 0 residues processed: 249 average time/residue: 0.4287 time to fit residues: 147.6331 Evaluate side-chains 113 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS W 285 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 424 GLN W 428 HIS ** W 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 591 GLN W 622 GLN W 667 ASN W 712 HIS ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1065 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3173 moved from start: 0.9013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 20705 Z= 0.529 Angle : 1.178 15.225 29338 Z= 0.634 Chirality : 0.058 0.443 3290 Planarity : 0.011 0.130 2604 Dihedral : 29.565 176.424 5335 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 33.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.53 % Favored : 93.35 % Rotamer: Outliers : 0.93 % Allowed : 5.07 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.18), residues: 1578 helix: -1.64 (0.15), residues: 906 sheet: -1.84 (0.59), residues: 70 loop : -3.02 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP W 793 HIS 0.018 0.004 HIS W 428 PHE 0.041 0.005 PHE C 25 TYR 0.047 0.005 TYR A 99 ARG 0.033 0.002 ARG W 688 *********************** 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 206 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.5990 (mt) cc_final: 0.5569 (mt) REVERT: C 68 ASN cc_start: 0.8709 (m-40) cc_final: 0.8500 (m110) REVERT: D 59 MET cc_start: 0.5322 (tpt) cc_final: 0.3978 (ttt) REVERT: D 103 LEU cc_start: 0.6106 (mt) cc_final: 0.5467 (mm) REVERT: D 105 LYS cc_start: 0.8293 (mmpt) cc_final: 0.8000 (tppt) REVERT: F 84 MET cc_start: -0.0049 (mmp) cc_final: -0.0415 (mmp) REVERT: W 244 ASN cc_start: 0.6803 (p0) cc_final: 0.5802 (p0) REVERT: W 364 LEU cc_start: 0.3077 (mt) cc_final: 0.2814 (mt) REVERT: W 384 ILE cc_start: 0.2963 (OUTLIER) cc_final: 0.2379 (tp) REVERT: W 387 MET cc_start: 0.6651 (mtp) cc_final: 0.5975 (mtp) REVERT: W 457 MET cc_start: 0.0458 (mtp) cc_final: 0.0165 (mtp) REVERT: W 681 MET cc_start: 0.5917 (tpt) cc_final: 0.5475 (tmm) REVERT: W 802 MET cc_start: 0.1318 (ttm) cc_final: 0.0733 (tpp) REVERT: W 834 ARG cc_start: 0.7542 (ppt170) cc_final: 0.7012 (ptm-80) outliers start: 13 outliers final: 5 residues processed: 203 average time/residue: 0.3944 time to fit residues: 113.4507 Evaluate side-chains 126 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 0.0070 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 0.0670 chunk 137 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 104 GLN E 108 ASN F 75 HIS G 38 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 ASN W 210 ASN W 337 HIS ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 719 GLN W 810 GLN W1065 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2863 moved from start: 0.8935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20705 Z= 0.184 Angle : 0.621 8.237 29338 Z= 0.349 Chirality : 0.039 0.292 3290 Planarity : 0.005 0.065 2604 Dihedral : 28.957 175.815 5335 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1578 helix: -0.35 (0.16), residues: 933 sheet: -1.35 (0.71), residues: 57 loop : -2.73 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP W 417 HIS 0.006 0.001 HIS W1065 PHE 0.032 0.002 PHE H 62 TYR 0.020 0.002 TYR H 118 ARG 0.012 0.001 ARG W 671 *********************** 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 161 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.610 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: H 62 PHE cc_start: 0.6476 (m-80) cc_final: 0.6152 (m-80) REVERT: W 364 LEU cc_start: 0.4128 (mt) cc_final: 0.3668 (mt) REVERT: W 387 MET cc_start: 0.6717 (mtp) cc_final: 0.6052 (mtp) REVERT: W 457 MET cc_start: 0.0895 (mtp) cc_final: 0.0560 (mtp) REVERT: W 802 MET cc_start: 0.1190 (ttm) cc_final: 0.0505 (tpp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.3805 time to fit residues: 89.0113 Evaluate side-chains 110 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 10.9990 chunk 162 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS W 205 ASN ** W 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN W 756 HIS W 779 ASN W 806 HIS W1145 ASN W1169 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4200 moved from start: 1.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 20705 Z= 0.477 Angle : 1.096 20.210 29338 Z= 0.599 Chirality : 0.054 0.321 3290 Planarity : 0.011 0.151 2604 Dihedral : 29.771 176.483 5335 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 36.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.05 % Favored : 91.76 % Rotamer: Outliers : 0.50 % Allowed : 5.36 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1578 helix: -1.44 (0.15), residues: 911 sheet: -2.24 (0.68), residues: 55 loop : -2.79 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP W 417 HIS 0.035 0.004 HIS G 31 PHE 0.047 0.004 PHE H 67 TYR 0.041 0.005 TYR F 51 ARG 0.037 0.002 ARG F 36 *********************** 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 219 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.1705 (m-80) cc_final: 0.0923 (p90) REVERT: B 84 MET cc_start: 0.6202 (mpp) cc_final: 0.5578 (mpp) REVERT: C 74 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7578 (mtmm) REVERT: D 59 MET cc_start: 0.8231 (tpt) cc_final: 0.7536 (mmp) REVERT: D 73 GLU cc_start: 0.7623 (tp30) cc_final: 0.7176 (tt0) REVERT: D 105 LYS cc_start: 0.8677 (mmpt) cc_final: 0.8409 (tppt) REVERT: E 89 VAL cc_start: 0.6893 (t) cc_final: 0.6144 (t) REVERT: F 51 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7114 (p90) REVERT: H 37 TYR cc_start: 0.3345 (OUTLIER) cc_final: 0.1988 (m-80) REVERT: H 58 ILE cc_start: 0.4960 (mt) cc_final: 0.4658 (mt) REVERT: W 243 ASP cc_start: 0.7485 (m-30) cc_final: 0.6570 (m-30) REVERT: W 291 ILE cc_start: 0.4198 (mt) cc_final: 0.2987 (mt) REVERT: W 441 LEU cc_start: 0.6435 (tp) cc_final: 0.6222 (tp) REVERT: W 505 ILE cc_start: 0.6817 (mp) cc_final: 0.5540 (mp) REVERT: W 525 LEU cc_start: 0.7371 (pp) cc_final: 0.7082 (pp) REVERT: W 697 MET cc_start: 0.4179 (mtp) cc_final: 0.2918 (mtp) outliers start: 7 outliers final: 1 residues processed: 218 average time/residue: 0.3497 time to fit residues: 111.1323 Evaluate side-chains 134 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 chunk 135 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 64 ASN W 254 GLN W 285 HIS ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3868 moved from start: 1.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20705 Z= 0.195 Angle : 0.659 9.018 29338 Z= 0.372 Chirality : 0.040 0.213 3290 Planarity : 0.005 0.075 2604 Dihedral : 29.072 173.304 5335 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1578 helix: -0.39 (0.16), residues: 922 sheet: -1.98 (0.75), residues: 44 loop : -2.50 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP W 386 HIS 0.006 0.001 HIS A 113 PHE 0.019 0.002 PHE W 414 TYR 0.014 0.002 TYR W 730 ARG 0.011 0.001 ARG B 40 *********************** 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 206 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.795 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: B 61 PHE cc_start: 0.7428 (m-10) cc_final: 0.7139 (m-10) REVERT: B 84 MET cc_start: 0.5175 (mpp) cc_final: 0.4677 (mpp) REVERT: C 56 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7111 (mt-10) REVERT: C 74 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7447 (mtmm) REVERT: D 59 MET cc_start: 0.8165 (tpt) cc_final: 0.7238 (tpp) REVERT: D 73 GLU cc_start: 0.7631 (tp30) cc_final: 0.7308 (tt0) REVERT: D 105 LYS cc_start: 0.8334 (mmpt) cc_final: 0.8066 (tppt) REVERT: D 113 LYS cc_start: 0.9210 (pttm) cc_final: 0.8853 (ptpt) REVERT: E 89 VAL cc_start: 0.6623 (t) cc_final: 0.6405 (m) REVERT: E 90 MET cc_start: 0.7167 (pmm) cc_final: 0.6860 (pmm) REVERT: F 68 ASP cc_start: 0.6679 (m-30) cc_final: 0.6178 (m-30) REVERT: H 103 LEU cc_start: 0.5764 (mt) cc_final: 0.5230 (mt) REVERT: W 243 ASP cc_start: 0.7151 (m-30) cc_final: 0.6605 (m-30) REVERT: W 510 MET cc_start: 0.5221 (tmm) cc_final: 0.5008 (tmm) REVERT: W 697 MET cc_start: 0.1746 (mtp) cc_final: 0.0932 (mtp) REVERT: W 701 ASP cc_start: 0.6083 (m-30) cc_final: 0.5335 (m-30) REVERT: W 778 ILE cc_start: 0.5352 (mm) cc_final: 0.5104 (mm) REVERT: W 802 MET cc_start: 0.2397 (mtt) cc_final: 0.1625 (tpp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3903 time to fit residues: 118.1334 Evaluate side-chains 138 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 106 HIS E 68 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4060 moved from start: 1.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20705 Z= 0.208 Angle : 0.648 11.861 29338 Z= 0.364 Chirality : 0.039 0.173 3290 Planarity : 0.005 0.064 2604 Dihedral : 28.812 178.523 5335 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 0.21 % Allowed : 2.14 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1578 helix: 0.03 (0.17), residues: 923 sheet: -1.95 (0.74), residues: 48 loop : -2.38 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP W 386 HIS 0.007 0.001 HIS C 82 PHE 0.020 0.002 PHE W 414 TYR 0.023 0.002 TYR B 72 ARG 0.011 0.001 ARG B 40 *********************** 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 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6774 (mt) cc_final: 0.5682 (mt) REVERT: A 100 LEU cc_start: 0.8694 (mt) cc_final: 0.8214 (mt) REVERT: A 113 HIS cc_start: 0.7913 (m170) cc_final: 0.7446 (m-70) REVERT: C 74 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7540 (mtmm) REVERT: D 59 MET cc_start: 0.8753 (tpt) cc_final: 0.8138 (tpp) REVERT: D 105 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8207 (tppt) REVERT: D 113 LYS cc_start: 0.9226 (pttm) cc_final: 0.8938 (ptpt) REVERT: E 89 VAL cc_start: 0.7229 (t) cc_final: 0.6757 (m) REVERT: E 90 MET cc_start: 0.7180 (pmm) cc_final: 0.6910 (pmm) REVERT: H 58 ILE cc_start: 0.3826 (tt) cc_final: 0.2576 (tt) REVERT: H 64 ASN cc_start: 0.6204 (m-40) cc_final: 0.5456 (m-40) REVERT: W 510 MET cc_start: 0.5565 (tmm) cc_final: 0.5102 (tmm) REVERT: W 802 MET cc_start: 0.3151 (mtt) cc_final: 0.1359 (mmm) outliers start: 3 outliers final: 0 residues processed: 216 average time/residue: 0.3535 time to fit residues: 114.3559 Evaluate side-chains 153 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 79 HIS W 222 HIS W 285 HIS ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 812 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 1.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20705 Z= 0.271 Angle : 0.745 9.363 29338 Z= 0.413 Chirality : 0.041 0.161 3290 Planarity : 0.006 0.088 2604 Dihedral : 28.901 176.480 5335 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1578 helix: -0.27 (0.16), residues: 922 sheet: -1.17 (0.70), residues: 53 loop : -2.47 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP W 417 HIS 0.008 0.002 HIS H 46 PHE 0.033 0.003 PHE H 62 TYR 0.035 0.003 TYR D 37 ARG 0.014 0.001 ARG B 40 *********************** 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 252 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.7974 (mt) cc_final: 0.6571 (mp) REVERT: A 106 ASP cc_start: 0.8464 (m-30) cc_final: 0.8049 (m-30) REVERT: A 107 THR cc_start: 0.7906 (m) cc_final: 0.7678 (m) REVERT: B 91 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8489 (mtpt) REVERT: C 74 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7996 (mtmm) REVERT: D 59 MET cc_start: 0.8840 (tpt) cc_final: 0.8239 (tpp) REVERT: D 63 VAL cc_start: 0.9241 (t) cc_final: 0.8987 (t) REVERT: D 109 SER cc_start: 0.8549 (m) cc_final: 0.8115 (p) REVERT: E 90 MET cc_start: 0.7763 (pmm) cc_final: 0.7360 (pmm) REVERT: E 130 ILE cc_start: 0.7723 (mt) cc_final: 0.7010 (mt) REVERT: E 131 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6918 (ttp-170) REVERT: F 70 VAL cc_start: 0.8386 (t) cc_final: 0.6757 (t) REVERT: G 102 ILE cc_start: 0.6971 (tp) cc_final: 0.6530 (tp) REVERT: W 327 ILE cc_start: 0.5765 (mm) cc_final: 0.5363 (mm) REVERT: W 787 VAL cc_start: 0.6757 (t) cc_final: 0.6542 (t) REVERT: W 802 MET cc_start: 0.3450 (mtt) cc_final: 0.1163 (mmm) REVERT: W 815 MET cc_start: 0.3518 (tpt) cc_final: 0.2407 (tmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3512 time to fit residues: 130.6259 Evaluate side-chains 178 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 55 GLN E 68 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 222 HIS W 285 HIS W 428 HIS W 779 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4571 moved from start: 1.9428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20705 Z= 0.209 Angle : 0.661 8.788 29338 Z= 0.370 Chirality : 0.039 0.189 3290 Planarity : 0.005 0.071 2604 Dihedral : 28.691 179.728 5335 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1578 helix: 0.11 (0.17), residues: 918 sheet: -1.21 (0.69), residues: 53 loop : -2.31 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 386 HIS 0.020 0.002 HIS G 82 PHE 0.020 0.002 PHE E 78 TYR 0.027 0.002 TYR H 118 ARG 0.013 0.001 ARG A 69 *********************** 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 238 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7043 (mm110) cc_final: 0.6371 (mm110) REVERT: A 100 LEU cc_start: 0.9143 (mt) cc_final: 0.8421 (mt) REVERT: B 91 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8277 (mmtp) REVERT: C 36 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8141 (tptp) REVERT: C 74 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8364 (mtmm) REVERT: C 94 ASN cc_start: 0.8475 (t0) cc_final: 0.8152 (t0) REVERT: D 48 ASP cc_start: 0.7949 (p0) cc_final: 0.7538 (t70) REVERT: D 59 MET cc_start: 0.8831 (tpt) cc_final: 0.8228 (tpp) REVERT: E 90 MET cc_start: 0.7515 (pmm) cc_final: 0.7283 (pmm) REVERT: F 84 MET cc_start: 0.2586 (mmp) cc_final: 0.2093 (ptp) REVERT: G 35 ARG cc_start: 0.7714 (ppt170) cc_final: 0.6937 (ptp-170) REVERT: G 84 GLN cc_start: 0.6123 (tp-100) cc_final: 0.5766 (tp-100) REVERT: G 88 ARG cc_start: 0.6995 (mmt180) cc_final: 0.6672 (mmp-170) REVERT: H 62 PHE cc_start: 0.7720 (m-80) cc_final: 0.6439 (p90) REVERT: W 244 ASN cc_start: 0.7183 (p0) cc_final: 0.5830 (t0) REVERT: W 387 MET cc_start: 0.5943 (mtm) cc_final: 0.5579 (mtm) REVERT: W 802 MET cc_start: 0.4698 (mtt) cc_final: 0.1525 (mmm) REVERT: W 815 MET cc_start: 0.4433 (tpt) cc_final: 0.2857 (tmm) REVERT: W 1123 LYS cc_start: -0.0788 (mmtt) cc_final: -0.1828 (ptmm) REVERT: W 1144 LYS cc_start: 0.2627 (mmtt) cc_final: 0.2247 (pttp) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3628 time to fit residues: 126.1479 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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: 9.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 0.0870 chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4836 moved from start: 2.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20705 Z= 0.229 Angle : 0.710 11.705 29338 Z= 0.392 Chirality : 0.040 0.208 3290 Planarity : 0.006 0.076 2604 Dihedral : 28.646 178.635 5335 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1578 helix: 0.06 (0.17), residues: 921 sheet: -0.98 (0.70), residues: 53 loop : -2.32 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP W 417 HIS 0.007 0.001 HIS A 113 PHE 0.021 0.002 PHE W 676 TYR 0.036 0.002 TYR C 50 ARG 0.012 0.001 ARG B 40 *********************** 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 247 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.700 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: A 63 ARG cc_start: 0.5100 (mpp-170) cc_final: 0.3572 (mmt90) REVERT: A 83 ARG cc_start: 0.7212 (mmt-90) cc_final: 0.6689 (ttt180) REVERT: A 100 LEU cc_start: 0.9157 (mt) cc_final: 0.8791 (mt) REVERT: A 107 THR cc_start: 0.8776 (m) cc_final: 0.8466 (p) REVERT: B 52 GLU cc_start: 0.7996 (tp30) cc_final: 0.7187 (tp30) REVERT: C 36 LYS cc_start: 0.8406 (ptpt) cc_final: 0.8015 (tptp) REVERT: C 94 ASN cc_start: 0.8284 (t0) cc_final: 0.8008 (t0) REVERT: D 59 MET cc_start: 0.8954 (tpt) cc_final: 0.8443 (mmp) REVERT: D 63 VAL cc_start: 0.9248 (t) cc_final: 0.9005 (t) REVERT: D 73 GLU cc_start: 0.8768 (tp30) cc_final: 0.8436 (tp30) REVERT: D 109 SER cc_start: 0.8805 (m) cc_final: 0.8330 (p) REVERT: D 110 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 53 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6982 (mtp85) REVERT: F 67 ARG cc_start: 0.8353 (tpm170) cc_final: 0.7973 (tpp-160) REVERT: F 70 VAL cc_start: 0.8480 (t) cc_final: 0.7777 (t) REVERT: W 802 MET cc_start: 0.4819 (mtt) cc_final: 0.1834 (mmm) REVERT: W 815 MET cc_start: 0.4735 (tpt) cc_final: 0.3205 (tmm) REVERT: W 1123 LYS cc_start: -0.0455 (mmtt) cc_final: -0.1693 (ptmm) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3683 time to fit residues: 133.1511 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 222 HIS W 285 HIS W 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5154 moved from start: 2.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 20705 Z= 0.281 Angle : 0.780 10.730 29338 Z= 0.432 Chirality : 0.045 0.540 3290 Planarity : 0.007 0.144 2604 Dihedral : 28.797 178.985 5335 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 0.14 % Allowed : 0.50 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1578 helix: -0.33 (0.16), residues: 938 sheet: -1.36 (0.64), residues: 59 loop : -2.35 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP W 417 HIS 0.009 0.002 HIS H 79 PHE 0.037 0.003 PHE W 414 TYR 0.043 0.003 TYR D 34 ARG 0.016 0.001 ARG B 78 ********************** 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 244 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 1.679 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: A 59 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8874 (mp0) REVERT: A 63 ARG cc_start: 0.5908 (mpp-170) cc_final: 0.5043 (mpt180) REVERT: A 94 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 107 THR cc_start: 0.9303 (m) cc_final: 0.8974 (p) REVERT: A 110 CYS cc_start: 0.8891 (m) cc_final: 0.7626 (t) REVERT: B 91 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8785 (mmtp) REVERT: C 25 PHE cc_start: 0.5269 (m-80) cc_final: 0.4786 (m-80) REVERT: C 36 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8365 (tptp) REVERT: C 61 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7876 (mt-10) REVERT: C 94 ASN cc_start: 0.8802 (t0) cc_final: 0.8442 (t0) REVERT: D 59 MET cc_start: 0.8873 (tpt) cc_final: 0.8590 (mmp) REVERT: D 105 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8291 (tppt) REVERT: D 109 SER cc_start: 0.9002 (m) cc_final: 0.8731 (p) REVERT: D 117 LYS cc_start: 0.8836 (tptt) cc_final: 0.8402 (ptmm) REVERT: E 53 ARG cc_start: 0.7888 (ttp-110) cc_final: 0.7590 (mtp85) REVERT: E 104 PHE cc_start: 0.7123 (t80) cc_final: 0.6854 (t80) REVERT: E 106 ASP cc_start: 0.8865 (t0) cc_final: 0.8586 (m-30) REVERT: E 130 ILE cc_start: 0.9266 (mm) cc_final: 0.8972 (mm) REVERT: F 84 MET cc_start: 0.6871 (ptp) cc_final: 0.6144 (pmm) REVERT: F 97 LEU cc_start: 0.5820 (mm) cc_final: 0.5359 (pt) REVERT: G 38 ASN cc_start: 0.4488 (OUTLIER) cc_final: 0.3961 (m110) REVERT: W 438 PRO cc_start: 0.7219 (Cg_endo) cc_final: 0.6620 (Cg_exo) REVERT: W 451 LEU cc_start: 0.5900 (mt) cc_final: 0.4871 (mp) REVERT: W 802 MET cc_start: 0.6153 (mtt) cc_final: 0.4039 (mmt) REVERT: W 815 MET cc_start: 0.5148 (tpt) cc_final: 0.4074 (tmm) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.3473 time to fit residues: 123.5020 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 106 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS W1065 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.075758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057831 restraints weight = 174348.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059252 restraints weight = 108840.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060250 restraints weight = 75224.243| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 2.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20705 Z= 0.270 Angle : 0.757 10.544 29338 Z= 0.421 Chirality : 0.043 0.293 3290 Planarity : 0.007 0.082 2604 Dihedral : 28.793 177.696 5335 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1578 helix: -0.15 (0.16), residues: 932 sheet: -0.91 (0.70), residues: 53 loop : -2.29 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP W 417 HIS 0.007 0.002 HIS W 428 PHE 0.023 0.002 PHE A 67 TYR 0.036 0.003 TYR W 316 ARG 0.012 0.001 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.17 seconds wall clock time: 71 minutes 32.34 seconds (4292.34 seconds total)