Starting phenix.real_space_refine on Wed Nov 19 06:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705.map" model { file = "/net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klb_0705/11_2025/6klb_0705_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 62 5.16 5 C 13519 2.51 5 N 3518 2.21 5 O 4231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21384 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 9206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1118, 9197 Classifications: {'peptide': 1118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1096} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1118, 9197 Classifications: {'peptide': 1118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1096} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 9369 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "D" Number of atoms: 9171 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1115, 9162 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1115, 9162 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 9332 Chain: "E" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 775 " occ=0.50 residue: pdb=" N ALYS D 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 775 " occ=0.50 Time building chain proxies: 7.70, per 1000 atoms: 0.36 Number of scatterers: 21384 At special positions: 0 Unit cell: (129.6, 185.76, 160.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 50 15.00 Mg 4 11.99 O 4231 8.00 N 3518 7.00 C 13519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS C 131 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4730 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 23 sheets defined 45.5% alpha, 9.5% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 25 through 33 removed outlier: 4.096A pdb=" N GLU A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 68 removed outlier: 4.463A pdb=" N SER A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.934A pdb=" N TYR A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.657A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 170 through 193 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 217 through 220 removed outlier: 3.586A pdb=" N PHE A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.961A pdb=" N PHE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.542A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.737A pdb=" N TYR A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.900A pdb=" N VAL A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.845A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.086A pdb=" N GLY A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.598A pdb=" N SER A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 4.091A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 472 Processing helix chain 'A' and resid 485 through 512 removed outlier: 4.015A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.954A pdb=" N LEU A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.830A pdb=" N PHE A 709 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 710 " --> pdb=" O LYS A 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 706 through 710' Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.604A pdb=" N LEU A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.563A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.896A pdb=" N GLU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 939 through 954 removed outlier: 3.594A pdb=" N TYR A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.407A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1200 Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 3.761A pdb=" N LEU A1206 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1225 Processing helix chain 'B' and resid 118 through 149 removed outlier: 3.603A pdb=" N LEU B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.822A pdb=" N LEU B 170 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.855A pdb=" N ARG B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.870A pdb=" N LEU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 149 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.958A pdb=" N LEU C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.060A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 204 " --> pdb=" O THR C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 37 through 66 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.737A pdb=" N TYR D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 111 Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.069A pdb=" N ILE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.808A pdb=" N GLU D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 148 through 162 removed outlier: 4.014A pdb=" N PHE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 193 removed outlier: 3.532A pdb=" N LYS D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 211 removed outlier: 3.581A pdb=" N LYS D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.719A pdb=" N PHE D 220 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.041A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 226' Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.483A pdb=" N ASN D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.565A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 330 Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 355 through 370 removed outlier: 4.249A pdb=" N ARG D 359 " --> pdb=" O TRP D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 393 removed outlier: 3.959A pdb=" N GLY D 393 " --> pdb=" O PHE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 409 through 431 removed outlier: 3.656A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 472 Processing helix chain 'D' and resid 485 through 512 removed outlier: 4.239A pdb=" N ASP D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR D 512 " --> pdb=" O ARG D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 564 removed outlier: 4.173A pdb=" N LYS D 564 " --> pdb=" O LYS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'D' and resid 718 through 726 removed outlier: 3.823A pdb=" N MET D 722 " --> pdb=" O ASN D 718 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 790 removed outlier: 3.727A pdb=" N PHE D 789 " --> pdb=" O ASP D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.581A pdb=" N GLU D 815 " --> pdb=" O LYS D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 885 Processing helix chain 'D' and resid 889 through 918 Processing helix chain 'D' and resid 939 through 954 removed outlier: 3.725A pdb=" N TYR D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 986 removed outlier: 3.822A pdb=" N MET D 986 " --> pdb=" O PHE D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1030 Processing helix chain 'D' and resid 1091 through 1101 Processing helix chain 'D' and resid 1114 through 1118 removed outlier: 3.944A pdb=" N GLN D1118 " --> pdb=" O LEU D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1136 Processing helix chain 'D' and resid 1178 through 1201 Processing helix chain 'D' and resid 1203 through 1208 Processing helix chain 'D' and resid 1215 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.689A pdb=" N TYR A 705 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.586A pdb=" N PHE A 244 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 252 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.904A pdb=" N PHE A 395 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 580 through 581 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 827 through 828 Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 924 through 925 removed outlier: 6.937A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1034 through 1037 Processing sheet with id=AB2, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AB4, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 181 removed outlier: 4.252A pdb=" N GLU C 180 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AB8, first strand: chain 'D' and resid 337 through 339 removed outlier: 3.907A pdb=" N PHE D 395 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 580 through 582 Processing sheet with id=AC1, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AC2, first strand: chain 'D' and resid 828 through 831 Processing sheet with id=AC3, first strand: chain 'D' and resid 858 through 863 Processing sheet with id=AC4, first strand: chain 'D' and resid 1031 through 1037 removed outlier: 6.465A pdb=" N PHE D1031 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D1048 " --> pdb=" O PHE D1031 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D1035 " --> pdb=" O GLU D1044 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D1044 " --> pdb=" O MET D1035 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D1037 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D1042 " --> pdb=" O VAL D1037 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1071 through 1073 895 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4352 1.33 - 1.45: 5505 1.45 - 1.58: 11836 1.58 - 1.70: 98 1.70 - 1.83: 102 Bond restraints: 21893 Sorted by residual: bond pdb=" N GLU B 219 " pdb=" CA GLU B 219 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.41e+00 bond pdb=" N ASP B 218 " pdb=" CA ASP B 218 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.89e+00 bond pdb=" C ASP C 192 " pdb=" N GLN C 193 " ideal model delta sigma weight residual 1.324 1.356 -0.032 1.38e-02 5.25e+03 5.49e+00 bond pdb=" C LYS D1101 " pdb=" O LYS D1101 " ideal model delta sigma weight residual 1.234 1.205 0.030 1.33e-02 5.65e+03 4.92e+00 bond pdb=" C VAL D 828 " pdb=" N ILE D 829 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.28e-02 6.10e+03 4.16e+00 ... (remaining 21888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 29253 3.03 - 6.06: 368 6.06 - 9.09: 60 9.09 - 12.12: 9 12.12 - 15.15: 1 Bond angle restraints: 29691 Sorted by residual: angle pdb=" N ALA A 920 " pdb=" CA ALA A 920 " pdb=" C ALA A 920 " ideal model delta sigma weight residual 109.07 124.22 -15.15 1.61e+00 3.86e-01 8.86e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 114.75 103.63 11.12 1.26e+00 6.30e-01 7.79e+01 angle pdb=" N ASN A 849 " pdb=" CA ASN A 849 " pdb=" C ASN A 849 " ideal model delta sigma weight residual 109.24 121.32 -12.08 1.67e+00 3.59e-01 5.24e+01 angle pdb=" N ILE A 922 " pdb=" CA ILE A 922 " pdb=" C ILE A 922 " ideal model delta sigma weight residual 109.45 118.57 -9.12 1.39e+00 5.18e-01 4.31e+01 angle pdb=" C LYS A 267 " pdb=" N GLN A 268 " pdb=" CA GLN A 268 " ideal model delta sigma weight residual 121.54 133.03 -11.49 1.91e+00 2.74e-01 3.62e+01 ... (remaining 29686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 13181 35.58 - 71.16: 165 71.16 - 106.73: 13 106.73 - 142.31: 0 142.31 - 177.89: 6 Dihedral angle restraints: 13365 sinusoidal: 6031 harmonic: 7334 Sorted by residual: dihedral pdb=" O4' C G 21 " pdb=" C1' C G 21 " pdb=" N1 C G 21 " pdb=" C2 C G 21 " ideal model delta sinusoidal sigma weight residual -128.00 49.89 -177.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -128.00 49.12 -177.12 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 14 " pdb=" C1' U E 14 " pdb=" N1 U E 14 " pdb=" C2 U E 14 " ideal model delta sinusoidal sigma weight residual -128.00 48.81 -176.81 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3021 0.098 - 0.196: 209 0.196 - 0.294: 12 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA ALA A 920 " pdb=" N ALA A 920 " pdb=" C ALA A 920 " pdb=" CB ALA A 920 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA GLU B 219 " pdb=" N GLU B 219 " pdb=" C GLU B 219 " pdb=" CB GLU B 219 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA ASN A 849 " pdb=" N ASN A 849 " pdb=" C ASN A 849 " pdb=" CB ASN A 849 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3243 not shown) Planarity restraints: 3615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 187 " -0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C ARG C 187 " 0.093 2.00e-02 2.50e+03 pdb=" O ARG C 187 " -0.035 2.00e-02 2.50e+03 pdb=" N TYR C 188 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D1101 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C LYS D1101 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS D1101 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR D1102 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 919 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ASP A 919 " -0.058 2.00e-02 2.50e+03 pdb=" O ASP A 919 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 920 " 0.019 2.00e-02 2.50e+03 ... (remaining 3612 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 194 2.59 - 3.17: 16997 3.17 - 3.75: 31314 3.75 - 4.32: 43929 4.32 - 4.90: 69312 Nonbonded interactions: 161746 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.015 2.170 nonbonded pdb="MG MG E1302 " pdb=" O HOH E1405 " model vdw 2.016 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.030 2.170 nonbonded pdb="MG MG E1302 " pdb=" O HOH E1403 " model vdw 2.031 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.036 2.170 ... (remaining 161741 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 1 through 584 or resid 680 through 774 or resid 776 throug \ h 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 through 1227)) selection = (chain 'D' and (resid 1 through 774 or resid 776 through 1227)) } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'E' and resid 1 through 1301) selection = chain 'G' } 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=0.50 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 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 : 0.004 0.057 21894 Z= 0.202 Angle : 0.901 15.152 29693 Z= 0.511 Chirality : 0.054 0.490 3246 Planarity : 0.006 0.076 3615 Dihedral : 12.494 177.889 8632 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.99 % Favored : 90.76 % Rotamer: Outliers : 0.31 % Allowed : 2.24 % Favored : 97.45 % Cbeta Deviations : 0.04 % 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: -5.01 (0.12), residues: 2453 helix: -3.34 (0.10), residues: 984 sheet: -2.14 (0.31), residues: 226 loop : -3.59 (0.13), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 206 TYR 0.019 0.002 TYR A 553 PHE 0.027 0.002 PHE A 709 TRP 0.039 0.003 TRP A 362 HIS 0.012 0.002 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00360 (21893) covalent geometry : angle 0.90100 (29691) SS BOND : bond 0.01242 ( 1) SS BOND : angle 2.07985 ( 2) hydrogen bonds : bond 0.13461 ( 905) hydrogen bonds : angle 11.31794 ( 2587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 632 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6875 (mtpt) cc_final: 0.6428 (mmtm) REVERT: A 132 LEU cc_start: 0.7316 (mt) cc_final: 0.6951 (mt) REVERT: A 479 GLU cc_start: 0.7494 (mm-30) cc_final: 0.5991 (pm20) REVERT: A 746 MET cc_start: 0.4124 (tmt) cc_final: 0.3789 (tpt) REVERT: A 836 ARG cc_start: 0.5905 (mtt-85) cc_final: 0.4676 (mtt180) REVERT: A 914 LEU cc_start: 0.8407 (mt) cc_final: 0.8195 (mt) REVERT: A 1167 TYR cc_start: 0.4808 (m-80) cc_final: 0.4510 (m-80) REVERT: C 152 TYR cc_start: 0.4799 (m-80) cc_final: 0.4596 (m-80) REVERT: C 217 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.4873 (ptt90) REVERT: D 124 ILE cc_start: 0.7933 (pt) cc_final: 0.7373 (pt) REVERT: D 257 GLU cc_start: 0.7424 (mp0) cc_final: 0.6987 (tm-30) REVERT: D 387 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8053 (mtpt) REVERT: D 429 TYR cc_start: 0.6482 (m-10) cc_final: 0.6271 (m-80) REVERT: D 841 ILE cc_start: 0.7900 (mm) cc_final: 0.7588 (mt) REVERT: D 957 MET cc_start: 0.6061 (ttp) cc_final: 0.5671 (tpt) outliers start: 7 outliers final: 1 residues processed: 638 average time/residue: 0.1925 time to fit residues: 179.1195 Evaluate side-chains 305 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 0.0040 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 268 GLN A 370 HIS A 714 HIS ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN A 864 ASN A 888 GLN A 889 ASN A 895 ASN A 989 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN C 181 GLN D 63 ASN D 100 ASN D 186 ASN D 468 ASN D 509 ASN D 735 GLN D 762 ASN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN D 837 ASN D 857 ASN D 888 GLN D1223 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.186285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.167453 restraints weight = 103255.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.170348 restraints weight = 98627.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.171057 restraints weight = 72768.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.172664 restraints weight = 46569.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.173876 restraints weight = 36663.707| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4776 r_free = 0.4776 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4776 r_free = 0.4776 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21894 Z= 0.138 Angle : 0.665 11.452 29693 Z= 0.356 Chirality : 0.042 0.205 3246 Planarity : 0.005 0.060 3615 Dihedral : 14.252 177.767 3452 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.52 (0.14), residues: 2453 helix: -1.53 (0.14), residues: 1007 sheet: -1.75 (0.33), residues: 220 loop : -3.22 (0.15), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 182 TYR 0.022 0.001 TYR A 183 PHE 0.031 0.002 PHE A 220 TRP 0.021 0.002 TRP A 362 HIS 0.004 0.001 HIS D 502 Details of bonding type rmsd covalent geometry : bond 0.00282 (21893) covalent geometry : angle 0.66505 (29691) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.43811 ( 2) hydrogen bonds : bond 0.05020 ( 905) hydrogen bonds : angle 6.80806 ( 2587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.4305 (tp40) cc_final: 0.3933 (tp40) REVERT: A 305 ARG cc_start: 0.4936 (mmt180) cc_final: 0.4537 (mtp180) REVERT: A 337 PHE cc_start: 0.7216 (m-80) cc_final: 0.6962 (m-80) REVERT: A 479 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6618 (mt-10) REVERT: A 836 ARG cc_start: 0.5484 (mtt-85) cc_final: 0.4442 (mtt180) REVERT: A 1062 LYS cc_start: 0.4837 (pptt) cc_final: 0.4180 (pptt) REVERT: A 1167 TYR cc_start: 0.4849 (m-80) cc_final: 0.4623 (m-80) REVERT: A 1199 LYS cc_start: 0.2875 (tptp) cc_final: 0.1917 (mttt) REVERT: C 132 ILE cc_start: 0.7627 (pt) cc_final: 0.7218 (tt) REVERT: D 52 LYS cc_start: 0.6869 (mmtp) cc_final: 0.6232 (ptmt) REVERT: D 429 TYR cc_start: 0.6583 (m-10) cc_final: 0.6280 (m-80) REVERT: D 841 ILE cc_start: 0.7765 (mm) cc_final: 0.7544 (mt) REVERT: D 944 GLN cc_start: 0.7473 (mt0) cc_final: 0.7006 (mm-40) REVERT: D 1025 LYS cc_start: 0.7919 (mttt) cc_final: 0.7555 (mmtt) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1814 time to fit residues: 111.0590 Evaluate side-chains 269 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 714 HIS A 762 ASN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN A 944 GLN A 989 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN C 142 GLN D 30 ASN D 96 ASN D 100 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 718 ASN D 735 GLN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D1139 ASN D1223 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.179087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.158843 restraints weight = 121023.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.164021 restraints weight = 138788.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.165714 restraints weight = 57223.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.166642 restraints weight = 42966.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.167471 restraints weight = 32499.115| |-----------------------------------------------------------------------------| r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4699 r_free = 0.4699 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4699 r_free = 0.4699 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21894 Z= 0.166 Angle : 0.693 12.282 29693 Z= 0.370 Chirality : 0.044 0.216 3246 Planarity : 0.005 0.053 3615 Dihedral : 14.174 175.157 3452 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.99 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.83 (0.15), residues: 2453 helix: -0.70 (0.15), residues: 1019 sheet: -1.63 (0.33), residues: 226 loop : -3.07 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 182 TYR 0.018 0.002 TYR A 903 PHE 0.031 0.002 PHE A 709 TRP 0.020 0.002 TRP A 362 HIS 0.011 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.00352 (21893) covalent geometry : angle 0.69283 (29691) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.88297 ( 2) hydrogen bonds : bond 0.05288 ( 905) hydrogen bonds : angle 6.18870 ( 2587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7293 (mppt) cc_final: 0.6849 (ttmt) REVERT: A 271 PRO cc_start: 0.3311 (Cg_exo) cc_final: 0.2516 (Cg_endo) REVERT: A 479 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6552 (tt0) REVERT: A 1044 GLU cc_start: 0.6611 (tp30) cc_final: 0.6316 (tp30) REVERT: A 1167 TYR cc_start: 0.4779 (m-80) cc_final: 0.4347 (m-80) REVERT: B 224 MET cc_start: 0.7156 (tmm) cc_final: 0.6896 (tmm) REVERT: C 132 ILE cc_start: 0.7611 (pt) cc_final: 0.7172 (tt) REVERT: C 152 TYR cc_start: 0.5065 (m-10) cc_final: 0.4761 (m-10) REVERT: D 52 LYS cc_start: 0.6745 (mmtp) cc_final: 0.6174 (ptmt) REVERT: D 429 TYR cc_start: 0.6559 (m-10) cc_final: 0.6071 (m-80) REVERT: D 737 ARG cc_start: 0.7416 (mmt180) cc_final: 0.6902 (mmm160) REVERT: D 841 ILE cc_start: 0.7961 (mm) cc_final: 0.7759 (mt) REVERT: D 858 GLU cc_start: 0.5403 (pt0) cc_final: 0.5033 (pt0) REVERT: D 934 SER cc_start: 0.7868 (t) cc_final: 0.7655 (t) REVERT: D 940 LYS cc_start: 0.6519 (pttm) cc_final: 0.6092 (pttt) REVERT: D 1025 LYS cc_start: 0.7980 (mttt) cc_final: 0.7606 (mmtt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1696 time to fit residues: 88.8998 Evaluate side-chains 240 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 221 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 163 optimal weight: 0.0470 chunk 233 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 HIS ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN D 502 HIS ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 HIS D 888 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.180415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.160357 restraints weight = 125591.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.165689 restraints weight = 142439.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.167511 restraints weight = 56703.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.168626 restraints weight = 41019.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.169652 restraints weight = 30808.671| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4725 r_free = 0.4725 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4725 r_free = 0.4725 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21894 Z= 0.133 Angle : 0.621 11.301 29693 Z= 0.333 Chirality : 0.042 0.205 3246 Planarity : 0.004 0.053 3615 Dihedral : 14.093 179.590 3452 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.31 (0.16), residues: 2453 helix: -0.13 (0.16), residues: 1021 sheet: -1.45 (0.33), residues: 228 loop : -2.91 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 222 TYR 0.017 0.001 TYR D1068 PHE 0.020 0.002 PHE A 709 TRP 0.017 0.002 TRP A 362 HIS 0.007 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.00273 (21893) covalent geometry : angle 0.62051 (29691) SS BOND : bond 0.00437 ( 1) SS BOND : angle 1.42832 ( 2) hydrogen bonds : bond 0.04768 ( 905) hydrogen bonds : angle 5.78204 ( 2587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.864 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: A 412 GLU cc_start: 0.7251 (tt0) cc_final: 0.6929 (tp30) REVERT: A 479 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6625 (tt0) REVERT: A 495 ASP cc_start: 0.6118 (p0) cc_final: 0.5328 (t70) REVERT: A 893 ILE cc_start: 0.8395 (mt) cc_final: 0.8163 (tp) REVERT: A 1074 ILE cc_start: 0.7051 (mp) cc_final: 0.6831 (mm) REVERT: A 1167 TYR cc_start: 0.4700 (m-80) cc_final: 0.4370 (m-80) REVERT: C 132 ILE cc_start: 0.7449 (pt) cc_final: 0.7057 (tt) REVERT: D 52 LYS cc_start: 0.7075 (mmtp) cc_final: 0.6347 (ptmt) REVERT: D 429 TYR cc_start: 0.6545 (m-10) cc_final: 0.6164 (m-80) REVERT: D 737 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6822 (mmm160) REVERT: D 893 ILE cc_start: 0.8562 (mt) cc_final: 0.8290 (tp) REVERT: D 1025 LYS cc_start: 0.8025 (mttt) cc_final: 0.7707 (mmtt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1770 time to fit residues: 91.3939 Evaluate side-chains 235 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 206 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS D 527 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D 889 ASN D 928 ASN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.177655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.157734 restraints weight = 119057.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.162674 restraints weight = 138942.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.163760 restraints weight = 62242.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.164459 restraints weight = 51665.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.164853 restraints weight = 37928.713| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4664 r_free = 0.4664 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4664 r_free = 0.4664 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21894 Z= 0.154 Angle : 0.659 10.873 29693 Z= 0.350 Chirality : 0.043 0.203 3246 Planarity : 0.004 0.050 3615 Dihedral : 14.050 177.748 3452 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.20 (0.16), residues: 2453 helix: 0.02 (0.16), residues: 1026 sheet: -1.67 (0.31), residues: 251 loop : -2.87 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 788 TYR 0.020 0.001 TYR A 903 PHE 0.027 0.002 PHE A 709 TRP 0.019 0.002 TRP A1063 HIS 0.007 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00322 (21893) covalent geometry : angle 0.65865 (29691) SS BOND : bond 0.01246 ( 1) SS BOND : angle 2.42611 ( 2) hydrogen bonds : bond 0.05052 ( 905) hydrogen bonds : angle 5.68926 ( 2587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.869 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 412 GLU cc_start: 0.7276 (tt0) cc_final: 0.7002 (tp30) REVERT: A 479 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6720 (tt0) REVERT: A 1074 ILE cc_start: 0.7191 (mp) cc_final: 0.6925 (mm) REVERT: A 1134 MET cc_start: 0.5547 (tmm) cc_final: 0.5296 (tmm) REVERT: A 1167 TYR cc_start: 0.4963 (m-80) cc_final: 0.4563 (m-80) REVERT: B 224 MET cc_start: 0.7292 (tmm) cc_final: 0.6880 (tmm) REVERT: C 132 ILE cc_start: 0.7562 (pt) cc_final: 0.7204 (tt) REVERT: C 152 TYR cc_start: 0.5113 (m-10) cc_final: 0.4815 (m-10) REVERT: D 52 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6351 (ptmt) REVERT: D 429 TYR cc_start: 0.6653 (m-10) cc_final: 0.5968 (m-80) REVERT: D 737 ARG cc_start: 0.7432 (mmt180) cc_final: 0.6949 (mmm160) REVERT: D 1025 LYS cc_start: 0.8151 (mttt) cc_final: 0.7817 (mmtt) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1651 time to fit residues: 82.3548 Evaluate side-chains 228 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 152 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 169 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 226 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D 888 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.177453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.156535 restraints weight = 115958.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.161070 restraints weight = 134700.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.162266 restraints weight = 65409.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.162841 restraints weight = 51115.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.165782 restraints weight = 40985.812| |-----------------------------------------------------------------------------| r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21894 Z= 0.144 Angle : 0.644 11.797 29693 Z= 0.342 Chirality : 0.043 0.198 3246 Planarity : 0.004 0.051 3615 Dihedral : 14.054 179.867 3452 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.06 (0.16), residues: 2453 helix: 0.18 (0.16), residues: 1024 sheet: -1.62 (0.31), residues: 247 loop : -2.83 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 222 TYR 0.016 0.001 TYR A 705 PHE 0.023 0.002 PHE A 709 TRP 0.015 0.002 TRP A1063 HIS 0.006 0.001 HIS D 797 Details of bonding type rmsd covalent geometry : bond 0.00303 (21893) covalent geometry : angle 0.64343 (29691) SS BOND : bond 0.00635 ( 1) SS BOND : angle 2.43496 ( 2) hydrogen bonds : bond 0.04862 ( 905) hydrogen bonds : angle 5.61178 ( 2587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 GLU cc_start: 0.7215 (tt0) cc_final: 0.6884 (tp30) REVERT: A 479 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6681 (tt0) REVERT: A 1074 ILE cc_start: 0.7235 (mp) cc_final: 0.6746 (mm) REVERT: A 1167 TYR cc_start: 0.4961 (m-80) cc_final: 0.4540 (m-80) REVERT: B 224 MET cc_start: 0.7348 (tmm) cc_final: 0.6843 (tmm) REVERT: C 132 ILE cc_start: 0.7410 (pt) cc_final: 0.7159 (tt) REVERT: C 152 TYR cc_start: 0.4963 (m-10) cc_final: 0.4757 (m-10) REVERT: D 52 LYS cc_start: 0.7206 (mmtp) cc_final: 0.6376 (ptpt) REVERT: D 429 TYR cc_start: 0.6572 (m-10) cc_final: 0.5922 (m-80) REVERT: D 722 MET cc_start: 0.3689 (ttt) cc_final: 0.3376 (ttt) REVERT: D 737 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6876 (mmm160) REVERT: D 893 ILE cc_start: 0.8392 (mt) cc_final: 0.8111 (tp) REVERT: D 1025 LYS cc_start: 0.8214 (mttt) cc_final: 0.7862 (mmtt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1689 time to fit residues: 82.1228 Evaluate side-chains 224 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 0.0370 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 837 ASN D 857 ASN D 888 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.178648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.158429 restraints weight = 109735.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.162520 restraints weight = 120085.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.163778 restraints weight = 60581.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.164325 restraints weight = 48512.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.165825 restraints weight = 38574.594| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4675 r_free = 0.4675 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4675 r_free = 0.4675 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21894 Z= 0.129 Angle : 0.625 10.831 29693 Z= 0.331 Chirality : 0.042 0.190 3246 Planarity : 0.004 0.052 3615 Dihedral : 14.004 178.546 3452 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.89 (0.16), residues: 2453 helix: 0.35 (0.16), residues: 1020 sheet: -1.51 (0.33), residues: 219 loop : -2.74 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 222 TYR 0.015 0.001 TYR A 705 PHE 0.020 0.001 PHE A 709 TRP 0.012 0.001 TRP A1063 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00267 (21893) covalent geometry : angle 0.62434 (29691) SS BOND : bond 0.00281 ( 1) SS BOND : angle 1.93942 ( 2) hydrogen bonds : bond 0.04645 ( 905) hydrogen bonds : angle 5.51991 ( 2587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.858 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 412 GLU cc_start: 0.7289 (tt0) cc_final: 0.6935 (tp30) REVERT: A 479 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6669 (tt0) REVERT: A 961 LYS cc_start: 0.4659 (mmmt) cc_final: 0.4235 (mmmt) REVERT: A 1062 LYS cc_start: 0.4750 (pptt) cc_final: 0.4194 (pptt) REVERT: A 1074 ILE cc_start: 0.7223 (mp) cc_final: 0.6844 (mm) REVERT: A 1167 TYR cc_start: 0.4973 (m-80) cc_final: 0.4537 (m-80) REVERT: B 122 LEU cc_start: 0.7015 (pp) cc_final: 0.6812 (pp) REVERT: B 224 MET cc_start: 0.7442 (tmm) cc_final: 0.6877 (tmm) REVERT: D 52 LYS cc_start: 0.7386 (mmtp) cc_final: 0.6547 (ptpt) REVERT: D 124 ILE cc_start: 0.7022 (pt) cc_final: 0.6811 (pt) REVERT: D 429 TYR cc_start: 0.6516 (m-10) cc_final: 0.5914 (m-80) REVERT: D 737 ARG cc_start: 0.7313 (mmt180) cc_final: 0.7020 (mmt180) REVERT: D 1025 LYS cc_start: 0.8232 (mttt) cc_final: 0.7896 (mmtt) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1683 time to fit residues: 80.3778 Evaluate side-chains 217 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 149 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 718 ASN A 732 ASN A 735 GLN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 873 HIS A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS D 527 ASN D 735 GLN ** D 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 944 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1166 ASN D1223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.169521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.150872 restraints weight = 131333.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.155380 restraints weight = 163275.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.156595 restraints weight = 60688.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.157588 restraints weight = 45930.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.158528 restraints weight = 33200.857| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4582 r_free = 0.4582 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4582 r_free = 0.4582 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21894 Z= 0.240 Angle : 0.835 17.588 29693 Z= 0.438 Chirality : 0.049 0.300 3246 Planarity : 0.005 0.059 3615 Dihedral : 14.442 175.799 3452 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.60 (0.16), residues: 2453 helix: -0.27 (0.15), residues: 1038 sheet: -2.22 (0.28), residues: 284 loop : -3.07 (0.16), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1138 TYR 0.027 0.003 TYR A 784 PHE 0.048 0.003 PHE A 745 TRP 0.030 0.003 TRP D 890 HIS 0.011 0.002 HIS D 797 Details of bonding type rmsd covalent geometry : bond 0.00523 (21893) covalent geometry : angle 0.83470 (29691) SS BOND : bond 0.01224 ( 1) SS BOND : angle 2.98508 ( 2) hydrogen bonds : bond 0.06303 ( 905) hydrogen bonds : angle 6.14961 ( 2587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.933 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: A 412 GLU cc_start: 0.7346 (tt0) cc_final: 0.7012 (tp30) REVERT: A 479 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6651 (tt0) REVERT: A 558 MET cc_start: 0.6045 (mpp) cc_final: 0.5651 (mpp) REVERT: A 1167 TYR cc_start: 0.5134 (m-80) cc_final: 0.4591 (m-80) REVERT: B 224 MET cc_start: 0.7860 (tmm) cc_final: 0.7182 (tmm) REVERT: D 52 LYS cc_start: 0.7442 (mmtp) cc_final: 0.6645 (ptpt) REVERT: D 124 ILE cc_start: 0.7021 (pt) cc_final: 0.6813 (pt) REVERT: D 187 MET cc_start: 0.0929 (ppp) cc_final: 0.0659 (ppp) REVERT: D 429 TYR cc_start: 0.6823 (m-10) cc_final: 0.6068 (m-80) REVERT: D 737 ARG cc_start: 0.7659 (mmt180) cc_final: 0.7076 (mmm160) REVERT: D 1025 LYS cc_start: 0.8201 (mttt) cc_final: 0.7838 (mmtt) REVERT: D 1223 GLN cc_start: 0.7883 (pt0) cc_final: 0.7568 (pp30) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1612 time to fit residues: 73.7610 Evaluate side-chains 212 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 106 optimal weight: 0.0070 chunk 195 optimal weight: 0.0980 chunk 13 optimal weight: 0.0060 chunk 230 optimal weight: 4.9990 chunk 218 optimal weight: 0.1980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN A 989 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D 944 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.178078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.158823 restraints weight = 131533.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.163896 restraints weight = 151301.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.165575 restraints weight = 57239.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.166644 restraints weight = 42265.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.167337 restraints weight = 30747.995| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4688 r_free = 0.4688 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4688 r_free = 0.4688 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21894 Z= 0.130 Angle : 0.648 11.013 29693 Z= 0.344 Chirality : 0.043 0.187 3246 Planarity : 0.004 0.057 3615 Dihedral : 14.130 175.966 3452 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.92 (0.16), residues: 2453 helix: 0.31 (0.16), residues: 1034 sheet: -1.49 (0.33), residues: 226 loop : -2.78 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 222 TYR 0.028 0.001 TYR D1185 PHE 0.029 0.002 PHE D 486 TRP 0.011 0.001 TRP A1218 HIS 0.021 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.00264 (21893) covalent geometry : angle 0.64759 (29691) SS BOND : bond 0.00411 ( 1) SS BOND : angle 4.11900 ( 2) hydrogen bonds : bond 0.04757 ( 905) hydrogen bonds : angle 5.55098 ( 2587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 GLU cc_start: 0.7082 (tt0) cc_final: 0.6877 (tp30) REVERT: A 558 MET cc_start: 0.5763 (mpp) cc_final: 0.5509 (mpp) REVERT: A 1062 LYS cc_start: 0.4582 (pptt) cc_final: 0.4081 (pptt) REVERT: A 1167 TYR cc_start: 0.5006 (m-80) cc_final: 0.4506 (m-80) REVERT: D 389 PHE cc_start: 0.3228 (t80) cc_final: 0.3006 (t80) REVERT: D 429 TYR cc_start: 0.6382 (m-10) cc_final: 0.5541 (m-80) REVERT: D 893 ILE cc_start: 0.8374 (mt) cc_final: 0.8120 (tp) REVERT: D 940 LYS cc_start: 0.6433 (pttm) cc_final: 0.6228 (pttt) REVERT: D 1025 LYS cc_start: 0.8098 (mttt) cc_final: 0.7870 (mmtt) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1605 time to fit residues: 78.7805 Evaluate side-chains 214 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 24 optimal weight: 0.0970 chunk 224 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 ASN A 888 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 30 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D 944 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.176797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.156571 restraints weight = 118500.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.161862 restraints weight = 140499.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.163570 restraints weight = 55569.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.163699 restraints weight = 53246.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.164943 restraints weight = 36480.358| |-----------------------------------------------------------------------------| r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4657 r_free = 0.4657 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4657 r_free = 0.4657 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21894 Z= 0.131 Angle : 0.653 12.025 29693 Z= 0.345 Chirality : 0.043 0.187 3246 Planarity : 0.004 0.054 3615 Dihedral : 14.054 177.803 3452 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.84 (0.16), residues: 2453 helix: 0.37 (0.16), residues: 1033 sheet: -1.38 (0.33), residues: 226 loop : -2.74 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 222 TYR 0.029 0.001 TYR D1185 PHE 0.022 0.002 PHE D1043 TRP 0.013 0.001 TRP D 355 HIS 0.005 0.001 HIS D 502 Details of bonding type rmsd covalent geometry : bond 0.00277 (21893) covalent geometry : angle 0.65242 (29691) SS BOND : bond 0.00537 ( 1) SS BOND : angle 3.95692 ( 2) hydrogen bonds : bond 0.04737 ( 905) hydrogen bonds : angle 5.50763 ( 2587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.811 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: A 412 GLU cc_start: 0.7142 (tt0) cc_final: 0.6907 (tp30) REVERT: A 531 MET cc_start: 0.7477 (ptm) cc_final: 0.7107 (ptm) REVERT: A 797 HIS cc_start: 0.1651 (m90) cc_final: 0.1417 (m90) REVERT: A 1062 LYS cc_start: 0.4568 (pptt) cc_final: 0.3117 (ptmt) REVERT: A 1128 MET cc_start: 0.4153 (mmp) cc_final: 0.3919 (mmm) REVERT: A 1167 TYR cc_start: 0.4977 (m-80) cc_final: 0.4473 (m-80) REVERT: C 152 TYR cc_start: 0.5059 (m-10) cc_final: 0.4716 (m-10) REVERT: D 419 ILE cc_start: 0.8156 (mt) cc_final: 0.7805 (mt) REVERT: D 429 TYR cc_start: 0.6510 (m-10) cc_final: 0.5893 (m-80) REVERT: D 1025 LYS cc_start: 0.8228 (mttt) cc_final: 0.7933 (mmtt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1572 time to fit residues: 70.6222 Evaluate side-chains 211 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 167 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D 944 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.175597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.156899 restraints weight = 104988.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.161243 restraints weight = 125183.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.161649 restraints weight = 59639.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.162158 restraints weight = 54400.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.163639 restraints weight = 40015.121| |-----------------------------------------------------------------------------| r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4654 r_free = 0.4654 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21894 Z= 0.142 Angle : 0.660 11.124 29693 Z= 0.350 Chirality : 0.043 0.202 3246 Planarity : 0.004 0.054 3615 Dihedral : 14.073 177.771 3452 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.82 (0.16), residues: 2453 helix: 0.31 (0.16), residues: 1046 sheet: -1.23 (0.34), residues: 206 loop : -2.72 (0.16), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 222 TYR 0.028 0.001 TYR D1185 PHE 0.023 0.002 PHE A 709 TRP 0.013 0.001 TRP D 355 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00304 (21893) covalent geometry : angle 0.65927 (29691) SS BOND : bond 0.00553 ( 1) SS BOND : angle 3.75698 ( 2) hydrogen bonds : bond 0.04824 ( 905) hydrogen bonds : angle 5.56555 ( 2587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3960.58 seconds wall clock time: 69 minutes 22.83 seconds (4162.83 seconds total)