Starting phenix.real_space_refine on Tue Nov 19 07:00:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/11_2024/7v01_26925_neut.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 51 5.16 5 C 11549 2.51 5 N 3112 2.21 5 O 3719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5636 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 7, 'TRANS': 685} Chain breaks: 3 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2386 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 12, 'rna3p': 12} Chain breaks: 1 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.68, per 1000 atoms: 0.63 Number of scatterers: 18492 At special positions: 0 Unit cell: (96.21, 118.659, 186.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 61 15.00 O 3719 8.00 N 3112 7.00 C 11549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3988 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 26 sheets defined 48.9% alpha, 16.0% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 6.42 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.532A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.991A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.743A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.763A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.537A pdb=" N PHE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.570A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.477A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.670A pdb=" N ASN E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.576A pdb=" N GLN E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 removed outlier: 3.522A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 231 Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 294 removed outlier: 3.762A pdb=" N ARG E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 296 No H-bonds generated for 'chain 'E' and resid 295 through 296' Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.995A pdb=" N MET E 300 " --> pdb=" O TYR E 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.712A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 24 removed outlier: 4.407A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 4.178A pdb=" N ARG F 30 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY F 31 " --> pdb=" O PHE F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.692A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 removed outlier: 4.388A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 122 removed outlier: 4.085A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 3.545A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.784A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 266 Processing helix chain 'F' and resid 273 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.572A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.508A pdb=" N ASN F 397 " --> pdb=" O ILE F 393 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 437 removed outlier: 4.143A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.647A pdb=" N ASN F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 550 through 567 Processing helix chain 'F' and resid 567 through 573 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 593 through 612 Processing helix chain 'F' and resid 630 through 636 Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 removed outlier: 3.664A pdb=" N ASN F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 734 Processing helix chain 'F' and resid 735 through 750 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.514A pdb=" N THR H 139 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.724A pdb=" N GLY H 194 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'I' and resid 15 through 24 Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.809A pdb=" N SER I 65 " --> pdb=" O ILE I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 removed outlier: 3.864A pdb=" N ILE I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 removed outlier: 3.809A pdb=" N SER K 65 " --> pdb=" O ILE K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 removed outlier: 3.865A pdb=" N ILE K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.504A pdb=" N VAL A 203 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 6 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR A 201 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER A 8 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 199 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR A 10 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 197 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU A 12 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LYS A 195 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.787A pdb=" N LEU A 43 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.551A pdb=" N LYS A 122 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 139 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.577A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.522A pdb=" N VAL B 156 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 4 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 10 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP B 196 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU B 12 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE B 194 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.556A pdb=" N ILE C 46 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.556A pdb=" N ILE C 46 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.818A pdb=" N ARG C 141 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.859A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 32 removed outlier: 3.679A pdb=" N LYS E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR E 95 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 193 removed outlier: 6.861A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR E 321 " --> pdb=" O ASN E 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.258A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 311 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 254 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.692A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 578 through 584 removed outlier: 6.734A pdb=" N PHE F 589 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER F 583 " --> pdb=" O ASP F 587 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP F 587 " --> pdb=" O SER F 583 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE F 625 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 623 " --> pdb=" O VAL F 528 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 530 " --> pdb=" O GLY F 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.825A pdb=" N VAL H 7 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE H 203 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC3, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC4, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC5, first strand: chain 'H' and resid 243 through 246 Processing sheet with id=AC6, first strand: chain 'H' and resid 281 through 284 Processing sheet with id=AC7, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.543A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.543A pdb=" N LYS K 26 " --> pdb=" O VAL K 38 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 6.12 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: 3874 1.33 - 1.45: 4726 1.45 - 1.57: 10139 1.57 - 1.70: 118 1.70 - 1.82: 90 Bond restraints: 18947 Sorted by residual: bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C5 ATP F 802 " pdb=" C6 ATP F 802 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" C4 ATP F 802 " pdb=" N9 ATP F 802 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C8 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 18942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 25454 3.28 - 6.57: 264 6.57 - 9.85: 23 9.85 - 13.14: 3 13.14 - 16.42: 5 Bond angle restraints: 25749 Sorted by residual: angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 123.45 16.42 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP F 802 " pdb=" O3A ATP F 802 " pdb=" PB ATP F 802 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 99.01 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" C4' A U 25 " pdb=" C3' A U 25 " pdb=" O3' A U 25 " ideal model delta sigma weight residual 113.00 97.76 15.24 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' U U 28 " pdb=" C3' U U 28 " pdb=" C2' U U 28 " ideal model delta sigma weight residual 109.50 124.01 -14.51 1.50e+00 4.44e-01 9.36e+01 ... (remaining 25744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11156 35.78 - 71.55: 277 71.55 - 107.33: 33 107.33 - 143.10: 3 143.10 - 178.88: 4 Dihedral angle restraints: 11473 sinusoidal: 5268 harmonic: 6205 Sorted by residual: dihedral pdb=" O4' U U 17 " pdb=" C1' U U 17 " pdb=" N1 U U 17 " pdb=" C2 U U 17 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U U 10 " pdb=" C1' U U 10 " pdb=" N1 U U 10 " pdb=" C2 U U 10 " ideal model delta sinusoidal sigma weight residual 232.00 75.77 156.23 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 7.04 -135.04 1 1.70e+01 3.46e-03 5.67e+01 ... (remaining 11470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2472 0.074 - 0.149: 337 0.149 - 0.223: 32 0.223 - 0.297: 6 0.297 - 0.371: 2 Chirality restraints: 2849 Sorted by residual: chirality pdb=" P G U 29 " pdb=" OP1 G U 29 " pdb=" OP2 G U 29 " pdb=" O5' G U 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' A U 25 " pdb=" C4' A U 25 " pdb=" O3' A U 25 " pdb=" C2' A U 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.83 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1' G G 21 " pdb=" O4' G G 21 " pdb=" C2' G G 21 " pdb=" N9 G G 21 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2846 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 540 " -0.061 2.00e-02 2.50e+03 4.57e-02 3.65e+01 pdb=" CG PHE F 540 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE F 540 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 540 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 540 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE F 540 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 540 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 14 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO E 15 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 43 " 0.059 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO A 44 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.048 5.00e-02 4.00e+02 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 66 2.44 - 3.05: 12282 3.05 - 3.67: 27339 3.67 - 4.28: 40610 4.28 - 4.90: 65946 Nonbonded interactions: 146243 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.822 3.120 nonbonded pdb=" OG SER B 86 " pdb=" O2' G G 5 " model vdw 2.070 3.040 nonbonded pdb=" OH TYR B 2 " pdb=" OE1 GLN H 45 " model vdw 2.177 3.040 nonbonded pdb=" OG SER I 46 " pdb=" OP2 U U 9 " model vdw 2.182 3.040 nonbonded pdb=" O2' G U 21 " pdb=" O5' C U 22 " model vdw 2.211 3.040 ... (remaining 146238 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 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.960 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.006 0.090 18947 Z= 0.359 Angle : 0.884 16.419 25749 Z= 0.535 Chirality : 0.052 0.371 2849 Planarity : 0.005 0.094 3088 Dihedral : 15.848 178.878 7482 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.47 % Allowed : 0.58 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2086 helix: -0.01 (0.16), residues: 926 sheet: -0.42 (0.28), residues: 321 loop : -1.75 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 339 HIS 0.007 0.001 HIS F 60 PHE 0.102 0.003 PHE F 540 TYR 0.055 0.002 TYR K 86 ARG 0.040 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 375 time to evaluate : 2.174 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: C 137 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6566 (ttm170) REVERT: E 119 MET cc_start: 0.7313 (tpp) cc_final: 0.6999 (tpp) REVERT: E 289 LEU cc_start: 0.7281 (mt) cc_final: 0.6794 (tt) REVERT: F 163 MET cc_start: 0.7443 (ptp) cc_final: 0.7050 (tpt) REVERT: F 588 LEU cc_start: 0.8293 (tp) cc_final: 0.8052 (tp) REVERT: F 697 MET cc_start: 0.7188 (mmm) cc_final: 0.6916 (mmm) REVERT: H 258 MET cc_start: -0.0037 (mmm) cc_final: -0.0583 (mmt) REVERT: I 43 LEU cc_start: 0.8394 (tp) cc_final: 0.8112 (tp) REVERT: I 58 LEU cc_start: 0.9499 (mt) cc_final: 0.9086 (mt) REVERT: I 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9092 (tp) REVERT: I 84 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9265 (mmmt) REVERT: I 120 PHE cc_start: 0.9357 (t80) cc_final: 0.9117 (t80) REVERT: K 75 ILE cc_start: 0.9334 (mm) cc_final: 0.8728 (mm) REVERT: K 77 GLU cc_start: 0.9211 (mm-30) cc_final: 0.9007 (mm-30) REVERT: K 87 TYR cc_start: 0.8289 (t80) cc_final: 0.6884 (t80) REVERT: K 137 TYR cc_start: 0.7843 (m-10) cc_final: 0.7469 (m-10) outliers start: 9 outliers final: 2 residues processed: 383 average time/residue: 0.4190 time to fit residues: 224.9970 Evaluate side-chains 168 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 384 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN E 54 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 560 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18947 Z= 0.256 Angle : 0.757 13.569 25749 Z= 0.401 Chirality : 0.046 0.273 2849 Planarity : 0.004 0.067 3088 Dihedral : 17.091 177.730 3199 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.95 % Allowed : 9.79 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2086 helix: 0.56 (0.17), residues: 948 sheet: -0.12 (0.29), residues: 309 loop : -1.72 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 339 HIS 0.007 0.001 HIS H 100 PHE 0.044 0.002 PHE I 85 TYR 0.028 0.002 TYR E 155 ARG 0.010 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.236 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: E 190 ARG cc_start: 0.7448 (mtm110) cc_final: 0.6944 (ttm110) REVERT: F 163 MET cc_start: 0.7405 (ptp) cc_final: 0.7046 (tpt) REVERT: F 588 LEU cc_start: 0.8416 (tp) cc_final: 0.8180 (tp) REVERT: F 624 MET cc_start: 0.3574 (tmm) cc_final: 0.2832 (tpp) REVERT: H 13 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6314 (pttm) REVERT: I 58 LEU cc_start: 0.9528 (mt) cc_final: 0.9222 (mt) REVERT: I 120 PHE cc_start: 0.9408 (t80) cc_final: 0.9122 (t80) REVERT: K 58 LEU cc_start: 0.9602 (mm) cc_final: 0.9264 (pp) REVERT: K 75 ILE cc_start: 0.9017 (mm) cc_final: 0.8780 (mm) REVERT: K 113 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8204 (pptt) REVERT: K 137 TYR cc_start: 0.8060 (m-10) cc_final: 0.7778 (m-80) outliers start: 37 outliers final: 16 residues processed: 210 average time/residue: 0.3610 time to fit residues: 111.1934 Evaluate side-chains 152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 18947 Z= 0.457 Angle : 0.843 13.837 25749 Z= 0.441 Chirality : 0.048 0.318 2849 Planarity : 0.005 0.069 3088 Dihedral : 17.059 178.495 3191 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.47 % Allowed : 11.42 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2086 helix: 0.36 (0.16), residues: 947 sheet: -0.53 (0.28), residues: 330 loop : -1.94 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 89 HIS 0.010 0.002 HIS K 18 PHE 0.045 0.003 PHE F 693 TYR 0.026 0.002 TYR E 155 ARG 0.008 0.001 ARG F 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 2.151 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: E 117 HIS cc_start: 0.6102 (t70) cc_final: 0.5708 (t70) REVERT: F 1 MET cc_start: 0.6342 (mmt) cc_final: 0.5943 (mmt) REVERT: F 163 MET cc_start: 0.8074 (ptp) cc_final: 0.7485 (tpt) REVERT: F 463 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6618 (p90) REVERT: F 624 MET cc_start: 0.4193 (tmm) cc_final: 0.3720 (tpp) REVERT: H 187 LEU cc_start: 0.8410 (mt) cc_final: 0.7962 (tt) REVERT: K 78 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9232 (mm) REVERT: K 103 LEU cc_start: 0.8814 (mt) cc_final: 0.8608 (mt) outliers start: 47 outliers final: 29 residues processed: 189 average time/residue: 0.3605 time to fit residues: 101.0367 Evaluate side-chains 156 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 206 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 196 ASN E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS H 17 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18947 Z= 0.229 Angle : 0.673 13.115 25749 Z= 0.357 Chirality : 0.044 0.309 2849 Planarity : 0.004 0.054 3088 Dihedral : 16.859 179.363 3191 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.16 % Allowed : 13.21 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2086 helix: 0.70 (0.17), residues: 945 sheet: -0.28 (0.30), residues: 314 loop : -1.79 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 52 HIS 0.010 0.001 HIS B 110 PHE 0.024 0.002 PHE I 85 TYR 0.026 0.001 TYR I 126 ARG 0.007 0.001 ARG F 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8851 (m) REVERT: F 163 MET cc_start: 0.7938 (ptp) cc_final: 0.7414 (tpt) REVERT: F 463 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6611 (p90) REVERT: F 624 MET cc_start: 0.3988 (tmm) cc_final: 0.3699 (tpp) REVERT: H 187 LEU cc_start: 0.8184 (mt) cc_final: 0.7832 (tt) REVERT: I 120 PHE cc_start: 0.9403 (t80) cc_final: 0.8947 (t80) REVERT: K 52 MET cc_start: 0.8167 (pmm) cc_final: 0.7966 (pmm) REVERT: K 72 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8818 (pm20) outliers start: 41 outliers final: 24 residues processed: 177 average time/residue: 0.3572 time to fit residues: 94.5490 Evaluate side-chains 148 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 3 optimal weight: 0.0270 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 40 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN H 129 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18947 Z= 0.385 Angle : 0.743 13.017 25749 Z= 0.395 Chirality : 0.046 0.334 2849 Planarity : 0.004 0.052 3088 Dihedral : 16.914 179.458 3191 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 13.00 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2086 helix: 0.61 (0.17), residues: 941 sheet: -0.63 (0.28), residues: 324 loop : -1.92 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 89 HIS 0.005 0.001 HIS F 230 PHE 0.023 0.002 PHE E 62 TYR 0.024 0.002 TYR E 155 ARG 0.016 0.001 ARG F 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6945 (mmtm) REVERT: E 40 MET cc_start: 0.8070 (mmp) cc_final: 0.7834 (mmp) REVERT: F 163 MET cc_start: 0.8190 (ptp) cc_final: 0.7956 (ptm) REVERT: F 352 MET cc_start: 0.7962 (mmm) cc_final: 0.7529 (mmm) REVERT: F 463 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6738 (p90) REVERT: F 697 MET cc_start: 0.4949 (mmm) cc_final: 0.4558 (mmm) REVERT: H 187 LEU cc_start: 0.8526 (mt) cc_final: 0.8070 (tt) REVERT: K 72 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8797 (pm20) REVERT: K 78 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9237 (mm) outliers start: 66 outliers final: 42 residues processed: 185 average time/residue: 0.3520 time to fit residues: 97.2277 Evaluate side-chains 157 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 40 GLN C 113 GLN C 161 GLN C 174 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18947 Z= 0.185 Angle : 0.648 12.923 25749 Z= 0.342 Chirality : 0.043 0.314 2849 Planarity : 0.003 0.050 3088 Dihedral : 16.716 179.161 3189 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.58 % Allowed : 14.84 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2086 helix: 0.82 (0.17), residues: 945 sheet: -0.61 (0.28), residues: 343 loop : -1.76 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 52 HIS 0.003 0.001 HIS E 117 PHE 0.018 0.001 PHE I 85 TYR 0.018 0.001 TYR H 184 ARG 0.008 0.001 ARG F 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 MET cc_start: 0.8004 (mmp) cc_final: 0.7667 (mmp) REVERT: F 163 MET cc_start: 0.8027 (ptp) cc_final: 0.7808 (ptm) REVERT: F 352 MET cc_start: 0.7824 (mmm) cc_final: 0.6617 (mmm) REVERT: F 463 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6625 (p90) REVERT: F 697 MET cc_start: 0.4772 (mmm) cc_final: 0.4491 (mmm) REVERT: H 187 LEU cc_start: 0.8308 (mt) cc_final: 0.7947 (tt) REVERT: K 72 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8742 (pm20) REVERT: K 95 VAL cc_start: 0.8661 (t) cc_final: 0.8438 (m) outliers start: 49 outliers final: 31 residues processed: 167 average time/residue: 0.3379 time to fit residues: 85.1741 Evaluate side-chains 147 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 255 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 127 optimal weight: 0.4980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN E 151 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN K 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18947 Z= 0.168 Angle : 0.638 13.016 25749 Z= 0.334 Chirality : 0.043 0.289 2849 Planarity : 0.003 0.047 3088 Dihedral : 16.468 178.547 3189 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.37 % Allowed : 15.74 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2086 helix: 0.89 (0.17), residues: 947 sheet: -0.42 (0.29), residues: 334 loop : -1.62 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 89 HIS 0.009 0.001 HIS K 18 PHE 0.017 0.001 PHE I 85 TYR 0.039 0.001 TYR K 126 ARG 0.007 0.000 ARG F 711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 2.329 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: E 40 MET cc_start: 0.7949 (mmp) cc_final: 0.7720 (mmp) REVERT: F 163 MET cc_start: 0.8046 (ptp) cc_final: 0.7811 (ptm) REVERT: F 257 MET cc_start: 0.7698 (mmt) cc_final: 0.7085 (mmm) REVERT: F 463 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6685 (p90) REVERT: F 588 LEU cc_start: 0.8512 (tp) cc_final: 0.8286 (tp) REVERT: F 624 MET cc_start: 0.4334 (OUTLIER) cc_final: 0.2438 (mpp) REVERT: F 697 MET cc_start: 0.4430 (mmm) cc_final: 0.4204 (mmm) REVERT: H 187 LEU cc_start: 0.8307 (mt) cc_final: 0.7981 (tt) REVERT: I 96 ASP cc_start: 0.8756 (m-30) cc_final: 0.8463 (m-30) REVERT: K 49 ARG cc_start: 0.7695 (ppt170) cc_final: 0.7377 (ppt170) REVERT: K 72 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: K 78 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9207 (mm) REVERT: K 97 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7424 (pt0) outliers start: 45 outliers final: 31 residues processed: 163 average time/residue: 0.3370 time to fit residues: 83.4222 Evaluate side-chains 148 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.0870 chunk 123 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18947 Z= 0.158 Angle : 0.641 13.002 25749 Z= 0.333 Chirality : 0.043 0.279 2849 Planarity : 0.003 0.046 3088 Dihedral : 16.343 179.135 3189 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 16.21 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2086 helix: 0.94 (0.17), residues: 942 sheet: -0.44 (0.28), residues: 356 loop : -1.46 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 89 HIS 0.010 0.001 HIS K 18 PHE 0.031 0.001 PHE K 120 TYR 0.016 0.001 TYR K 123 ARG 0.009 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 2.113 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: E 40 MET cc_start: 0.7897 (mmp) cc_final: 0.7651 (mmp) REVERT: F 163 MET cc_start: 0.8065 (ptp) cc_final: 0.7844 (ptm) REVERT: F 463 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6717 (p90) REVERT: F 588 LEU cc_start: 0.8443 (tp) cc_final: 0.8184 (tp) REVERT: F 624 MET cc_start: 0.4485 (OUTLIER) cc_final: 0.2621 (mpp) REVERT: I 96 ASP cc_start: 0.8743 (m-30) cc_final: 0.8458 (m-30) REVERT: K 49 ARG cc_start: 0.7566 (ppt170) cc_final: 0.7212 (ppt170) REVERT: K 72 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: K 78 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9181 (mm) outliers start: 41 outliers final: 30 residues processed: 156 average time/residue: 0.3387 time to fit residues: 80.2898 Evaluate side-chains 148 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 97 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18947 Z= 0.222 Angle : 0.661 12.955 25749 Z= 0.347 Chirality : 0.043 0.287 2849 Planarity : 0.003 0.048 3088 Dihedral : 16.243 178.819 3189 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.16 % Allowed : 16.58 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2086 helix: 1.00 (0.17), residues: 941 sheet: -0.44 (0.29), residues: 349 loop : -1.52 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 89 HIS 0.022 0.001 HIS F 165 PHE 0.048 0.001 PHE I 85 TYR 0.037 0.001 TYR K 126 ARG 0.009 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 2.398 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: E 40 MET cc_start: 0.7942 (mmp) cc_final: 0.7704 (mmp) REVERT: F 163 MET cc_start: 0.8111 (ptp) cc_final: 0.7879 (ptm) REVERT: F 463 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6839 (p90) REVERT: F 624 MET cc_start: 0.4386 (OUTLIER) cc_final: 0.2563 (mpp) REVERT: H 187 LEU cc_start: 0.8384 (mt) cc_final: 0.8045 (tt) REVERT: I 96 ASP cc_start: 0.8774 (m-30) cc_final: 0.8453 (m-30) REVERT: K 49 ARG cc_start: 0.7643 (ppt170) cc_final: 0.7370 (ppt170) REVERT: K 78 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 41 outliers final: 29 residues processed: 147 average time/residue: 0.3514 time to fit residues: 79.6929 Evaluate side-chains 140 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18947 Z= 0.180 Angle : 0.679 16.074 25749 Z= 0.348 Chirality : 0.044 0.331 2849 Planarity : 0.003 0.052 3088 Dihedral : 16.166 179.053 3189 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.74 % Allowed : 17.00 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2086 helix: 1.01 (0.17), residues: 942 sheet: -0.43 (0.29), residues: 346 loop : -1.47 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 89 HIS 0.007 0.001 HIS K 18 PHE 0.071 0.001 PHE E 62 TYR 0.022 0.001 TYR I 123 ARG 0.009 0.000 ARG K 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 2.456 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: C 72 HIS cc_start: 0.6424 (p90) cc_final: 0.6217 (p90) REVERT: E 186 MET cc_start: 0.6819 (tpp) cc_final: 0.6553 (mmt) REVERT: F 163 MET cc_start: 0.8101 (ptp) cc_final: 0.7878 (ptm) REVERT: F 463 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6795 (p90) REVERT: F 624 MET cc_start: 0.4269 (tpp) cc_final: 0.2451 (mpp) REVERT: H 187 LEU cc_start: 0.8336 (mt) cc_final: 0.8007 (tt) REVERT: I 96 ASP cc_start: 0.8755 (m-30) cc_final: 0.8431 (m-30) REVERT: K 49 ARG cc_start: 0.7575 (ppt170) cc_final: 0.7354 (ppt170) REVERT: K 78 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 33 outliers final: 28 residues processed: 143 average time/residue: 0.3525 time to fit residues: 76.7187 Evaluate side-chains 141 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 567 TYR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 114 ASN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 316 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN H 86 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.057153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044113 restraints weight = 130241.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.045471 restraints weight = 74563.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.046393 restraints weight = 51629.424| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18947 Z= 0.368 Angle : 0.790 19.165 25749 Z= 0.407 Chirality : 0.046 0.326 2849 Planarity : 0.005 0.143 3088 Dihedral : 16.386 179.152 3189 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.00 % Allowed : 17.21 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2086 helix: 0.78 (0.17), residues: 947 sheet: -0.53 (0.29), residues: 331 loop : -1.74 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 89 HIS 0.007 0.002 HIS K 18 PHE 0.084 0.002 PHE E 62 TYR 0.043 0.002 TYR K 126 ARG 0.024 0.001 ARG E 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.67 seconds wall clock time: 63 minutes 40.99 seconds (3820.99 seconds total)