Starting phenix.real_space_refine on Fri Feb 16 11:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/02_2024/7jk6_22363_updated.pdb" } resolution = 4.0 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 9657 2.51 5 N 2638 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15161 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3528 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 11, 'TRANS': 426} Chain breaks: 3 Chain: "E" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2974 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 5 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2919 Classifications: {'peptide': 373} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1328 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "C" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4173 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 20, 'TRANS': 499} Chain breaks: 6 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.89, per 1000 atoms: 0.52 Number of scatterers: 15161 At special positions: 0 Unit cell: (110.94, 149.64, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 82 16.00 P 9 15.00 Mg 3 11.99 O 2772 8.00 N 2638 7.00 C 9657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 8 sheets defined 57.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 63 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 156 through 166 removed outlier: 6.013A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.938A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.746A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.619A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.590A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Proline residue: E 10 - end of helix Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 111 removed outlier: 4.052A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.018A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.598A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 185 through 204 removed outlier: 4.472A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 223 through 237 Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.888A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 288 Proline residue: E 282 - end of helix removed outlier: 3.626A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 588 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 641 through 651 removed outlier: 3.979A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.748A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 removed outlier: 3.530A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.571A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 823 through 828 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.679A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 removed outlier: 4.294A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.062A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 88 removed outlier: 5.293A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.732A pdb=" N SER C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.516A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.490A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 575 Processing helix chain 'C' and resid 577 through 580 No H-bonds generated for 'chain 'C' and resid 577 through 580' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 599 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 4.205A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 237 Processing sheet with id= A, first strand: chain 'D' and resid 50 through 55 Processing sheet with id= B, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= C, first strand: chain 'E' and resid 176 through 180 removed outlier: 3.891A pdb=" N SER E 159 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY E 41 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.688A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 891 through 893 Processing sheet with id= F, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.443A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.613A pdb=" N ARG C 262 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 98 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 127 through 131 removed outlier: 5.984A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 702 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4802 1.34 - 1.46: 3285 1.46 - 1.58: 7212 1.58 - 1.71: 16 1.71 - 1.83: 118 Bond restraints: 15433 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C THR B 471 " pdb=" N PRO B 472 " ideal model delta sigma weight residual 1.334 1.388 -0.055 8.40e-03 1.42e+04 4.25e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.18e+01 ... (remaining 15428 not shown) Histogram of bond angle deviations from ideal: 96.37 - 104.26: 208 104.26 - 112.15: 7332 112.15 - 120.04: 7146 120.04 - 127.94: 6075 127.94 - 135.83: 121 Bond angle restraints: 20882 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 118.70 21.17 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.99 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.88 16.99 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 ... (remaining 20877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8401 17.95 - 35.90: 828 35.90 - 53.86: 152 53.86 - 71.81: 26 71.81 - 89.76: 16 Dihedral angle restraints: 9423 sinusoidal: 3888 harmonic: 5535 Sorted by residual: dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP C 337 " pdb=" C ASP C 337 " pdb=" N TYR C 338 " pdb=" CA TYR C 338 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N THR D 159 " pdb=" CA THR D 159 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 9420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2113 0.102 - 0.204: 281 0.204 - 0.306: 18 0.306 - 0.407: 3 0.407 - 0.509: 1 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB THR C 336 " pdb=" CA THR C 336 " pdb=" OG1 THR C 336 " pdb=" CG2 THR C 336 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" CB ILE E 123 " pdb=" CA ILE E 123 " pdb=" CG1 ILE E 123 " pdb=" CG2 ILE E 123 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA GLU E 260 " pdb=" N GLU E 260 " pdb=" C GLU E 260 " pdb=" CB GLU E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2413 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 324 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" CD GLU C 324 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU C 324 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU C 324 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 232 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LEU E 232 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU E 232 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE E 233 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 747 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C HIS A 747 " -0.067 2.00e-02 2.50e+03 pdb=" O HIS A 747 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A 748 " 0.023 2.00e-02 2.50e+03 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 83 2.55 - 3.14: 11350 3.14 - 3.73: 23864 3.73 - 4.31: 31846 4.31 - 4.90: 53394 Nonbonded interactions: 120537 Sorted by model distance: nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 1.967 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.140 2.170 nonbonded pdb=" O3G ATP A1001 " pdb="MG MG A1002 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.170 2.170 nonbonded pdb=" O2B ATP D 901 " pdb="MG MG D 902 " model vdw 2.179 2.170 ... (remaining 120532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 6.560 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 41.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.008 0.101 15433 Z= 0.510 Angle : 1.267 21.170 20882 Z= 0.741 Chirality : 0.070 0.509 2416 Planarity : 0.008 0.087 2642 Dihedral : 14.917 89.759 5809 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.24 % Allowed : 5.95 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.89 (0.16), residues: 1843 helix: -2.46 (0.10), residues: 1099 sheet: -2.88 (0.33), residues: 168 loop : 0.20 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 475 HIS 0.012 0.002 HIS E 412 PHE 0.030 0.004 PHE E 450 TYR 0.029 0.004 TYR C 255 ARG 0.008 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.968 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: D 23 TYR cc_start: 0.8450 (m-80) cc_final: 0.7820 (m-80) REVERT: D 79 PHE cc_start: 0.8139 (t80) cc_final: 0.7580 (t80) REVERT: D 102 SER cc_start: 0.9213 (t) cc_final: 0.8949 (p) REVERT: D 146 LEU cc_start: 0.9126 (mt) cc_final: 0.8683 (mt) REVERT: D 147 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8506 (mp0) REVERT: D 151 LEU cc_start: 0.9591 (tt) cc_final: 0.9145 (tt) REVERT: D 341 CYS cc_start: 0.8707 (t) cc_final: 0.8413 (m) REVERT: D 409 LEU cc_start: 0.9153 (tp) cc_final: 0.8905 (mp) REVERT: E 82 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8968 (mt-10) REVERT: E 164 GLU cc_start: 0.8902 (pt0) cc_final: 0.8489 (tm-30) REVERT: E 228 ASN cc_start: 0.9644 (t0) cc_final: 0.9270 (p0) REVERT: E 402 ASN cc_start: 0.9550 (m110) cc_final: 0.8881 (p0) REVERT: E 413 LEU cc_start: 0.8377 (mp) cc_final: 0.8039 (mp) REVERT: E 415 LEU cc_start: 0.8852 (mm) cc_final: 0.8626 (mm) REVERT: A 622 ASN cc_start: 0.9367 (t0) cc_final: 0.8915 (p0) REVERT: A 635 MET cc_start: 0.8918 (mmm) cc_final: 0.8098 (mmt) REVERT: A 720 MET cc_start: 0.9397 (tpt) cc_final: 0.9196 (tpp) REVERT: A 829 CYS cc_start: 0.8742 (m) cc_final: 0.8471 (m) REVERT: A 879 LEU cc_start: 0.9254 (mt) cc_final: 0.8887 (mt) REVERT: B 339 TYR cc_start: 0.8597 (m-10) cc_final: 0.8319 (m-80) REVERT: B 474 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8651 (pt) REVERT: B 488 TRP cc_start: 0.8221 (m100) cc_final: 0.7834 (m100) REVERT: C 51 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8889 (mp0) REVERT: C 189 LYS cc_start: 0.9729 (tttm) cc_final: 0.9524 (tptp) REVERT: C 212 PHE cc_start: 0.8799 (t80) cc_final: 0.8464 (t80) REVERT: C 221 GLN cc_start: 0.9668 (mt0) cc_final: 0.9361 (mp10) REVERT: C 384 TYR cc_start: 0.8916 (t80) cc_final: 0.8601 (t80) REVERT: C 625 MET cc_start: 0.7564 (mmt) cc_final: 0.6762 (tpt) outliers start: 4 outliers final: 2 residues processed: 324 average time/residue: 0.3110 time to fit residues: 142.8354 Evaluate side-chains 204 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 chunk 88 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 315 GLN E 107 GLN E 137 ASN E 433 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS C 615 HIS C 626 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15433 Z= 0.183 Angle : 0.684 9.871 20882 Z= 0.341 Chirality : 0.041 0.181 2416 Planarity : 0.005 0.060 2642 Dihedral : 7.969 76.614 2148 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.27 % Allowed : 12.32 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.92 (0.18), residues: 1843 helix: -0.41 (0.14), residues: 1105 sheet: -2.24 (0.36), residues: 162 loop : -0.05 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 191 HIS 0.010 0.001 HIS B 429 PHE 0.017 0.002 PHE C 49 TYR 0.025 0.002 TYR B 356 ARG 0.006 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 1.826 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: D 23 TYR cc_start: 0.8481 (m-80) cc_final: 0.7919 (m-80) REVERT: D 79 PHE cc_start: 0.8179 (t80) cc_final: 0.7476 (t80) REVERT: D 102 SER cc_start: 0.9189 (t) cc_final: 0.8888 (p) REVERT: D 148 GLU cc_start: 0.8502 (tt0) cc_final: 0.8253 (tt0) REVERT: D 324 MET cc_start: 0.9046 (mtp) cc_final: 0.8345 (ttm) REVERT: D 341 CYS cc_start: 0.8708 (t) cc_final: 0.8439 (m) REVERT: D 409 LEU cc_start: 0.9369 (tp) cc_final: 0.9001 (mp) REVERT: E 82 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9090 (mm-30) REVERT: E 228 ASN cc_start: 0.9659 (t0) cc_final: 0.9309 (p0) REVERT: E 402 ASN cc_start: 0.9465 (m110) cc_final: 0.9165 (p0) REVERT: E 415 LEU cc_start: 0.8733 (mm) cc_final: 0.8513 (mm) REVERT: A 552 LEU cc_start: 0.9362 (tp) cc_final: 0.8954 (pp) REVERT: A 622 ASN cc_start: 0.9297 (t0) cc_final: 0.8994 (p0) REVERT: A 635 MET cc_start: 0.8681 (mmm) cc_final: 0.7962 (mmt) REVERT: A 701 LEU cc_start: 0.9025 (tp) cc_final: 0.8800 (pp) REVERT: B 339 TYR cc_start: 0.8615 (m-10) cc_final: 0.8382 (m-10) REVERT: B 342 LYS cc_start: 0.9511 (tptt) cc_final: 0.9302 (tppt) REVERT: B 382 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6370 (p0) REVERT: B 488 TRP cc_start: 0.8436 (m100) cc_final: 0.7946 (m100) REVERT: C 51 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8855 (mp0) REVERT: C 128 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (mpp) REVERT: C 189 LYS cc_start: 0.9735 (tttm) cc_final: 0.9533 (tptp) REVERT: C 212 PHE cc_start: 0.8889 (t80) cc_final: 0.8354 (t80) REVERT: C 222 ASP cc_start: 0.9239 (m-30) cc_final: 0.8945 (p0) REVERT: C 384 TYR cc_start: 0.8709 (t80) cc_final: 0.8467 (t80) REVERT: C 388 LYS cc_start: 0.9286 (tptp) cc_final: 0.8889 (tptp) REVERT: C 425 LEU cc_start: 0.9231 (mp) cc_final: 0.8886 (tp) REVERT: C 429 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9054 (mp) REVERT: C 625 MET cc_start: 0.7403 (mmt) cc_final: 0.6695 (tpt) outliers start: 21 outliers final: 9 residues processed: 257 average time/residue: 0.2711 time to fit residues: 102.8909 Evaluate side-chains 207 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.0970 chunk 167 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS C 325 HIS C 591 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15433 Z= 0.198 Angle : 0.648 11.251 20882 Z= 0.321 Chirality : 0.041 0.209 2416 Planarity : 0.004 0.085 2642 Dihedral : 7.805 74.635 2146 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.70 % Allowed : 14.93 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.10 (0.19), residues: 1843 helix: 0.45 (0.15), residues: 1111 sheet: -1.86 (0.36), residues: 162 loop : -0.26 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 475 HIS 0.008 0.001 HIS D 437 PHE 0.021 0.001 PHE E 389 TYR 0.017 0.001 TYR D 239 ARG 0.006 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.654 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: D 79 PHE cc_start: 0.8387 (t80) cc_final: 0.7609 (t80) REVERT: D 102 SER cc_start: 0.9220 (t) cc_final: 0.8943 (p) REVERT: D 148 GLU cc_start: 0.8580 (tt0) cc_final: 0.8310 (tt0) REVERT: D 149 PHE cc_start: 0.8373 (t80) cc_final: 0.8157 (t80) REVERT: D 324 MET cc_start: 0.9082 (mtp) cc_final: 0.8419 (ttm) REVERT: D 404 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8513 (tp30) REVERT: D 409 LEU cc_start: 0.9359 (tp) cc_final: 0.8951 (mp) REVERT: E 78 LYS cc_start: 0.9402 (mmtt) cc_final: 0.8919 (tppt) REVERT: E 82 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9100 (mm-30) REVERT: E 101 MET cc_start: 0.9213 (pmm) cc_final: 0.8902 (pmm) REVERT: E 228 ASN cc_start: 0.9681 (t0) cc_final: 0.9347 (p0) REVERT: E 402 ASN cc_start: 0.9484 (m110) cc_final: 0.9137 (p0) REVERT: E 413 LEU cc_start: 0.8567 (mp) cc_final: 0.8339 (mp) REVERT: E 415 LEU cc_start: 0.8679 (mm) cc_final: 0.8465 (mm) REVERT: A 552 LEU cc_start: 0.9389 (tp) cc_final: 0.8965 (pp) REVERT: A 622 ASN cc_start: 0.9274 (t0) cc_final: 0.9034 (p0) REVERT: A 630 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9006 (mt) REVERT: A 635 MET cc_start: 0.8612 (mmm) cc_final: 0.8258 (mmt) REVERT: A 701 LEU cc_start: 0.9002 (tp) cc_final: 0.8796 (pp) REVERT: A 807 MET cc_start: 0.8836 (mmp) cc_final: 0.8619 (mmp) REVERT: A 853 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 342 LYS cc_start: 0.9513 (tptt) cc_final: 0.9289 (tppt) REVERT: B 388 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.6855 (mt) REVERT: B 393 MET cc_start: 0.8431 (mpp) cc_final: 0.7652 (pmm) REVERT: B 488 TRP cc_start: 0.8489 (m100) cc_final: 0.8060 (m100) REVERT: C 51 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8788 (mp0) REVERT: C 128 MET cc_start: 0.8949 (mpp) cc_final: 0.8713 (mpp) REVERT: C 189 LYS cc_start: 0.9727 (tttm) cc_final: 0.9520 (tptp) REVERT: C 221 GLN cc_start: 0.9638 (mt0) cc_final: 0.9312 (mp10) REVERT: C 222 ASP cc_start: 0.9260 (m-30) cc_final: 0.9024 (p0) REVERT: C 326 PHE cc_start: 0.8139 (m-80) cc_final: 0.7671 (t80) REVERT: C 388 LYS cc_start: 0.9259 (tptp) cc_final: 0.9021 (tptp) REVERT: C 425 LEU cc_start: 0.9263 (mp) cc_final: 0.8998 (tp) REVERT: C 429 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9121 (mp) REVERT: C 625 MET cc_start: 0.7264 (mmt) cc_final: 0.6649 (tpt) outliers start: 28 outliers final: 20 residues processed: 217 average time/residue: 0.2642 time to fit residues: 87.6845 Evaluate side-chains 199 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 0.0470 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15433 Z= 0.151 Angle : 0.617 14.046 20882 Z= 0.297 Chirality : 0.039 0.161 2416 Planarity : 0.003 0.047 2642 Dihedral : 7.617 72.001 2146 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.00 % Allowed : 15.72 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.24 (0.19), residues: 1843 helix: 0.77 (0.16), residues: 1113 sheet: -1.61 (0.36), residues: 162 loop : -0.28 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 475 HIS 0.005 0.001 HIS A 914 PHE 0.020 0.001 PHE C 212 TYR 0.022 0.001 TYR A 579 ARG 0.009 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 1.820 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: D 79 PHE cc_start: 0.8467 (t80) cc_final: 0.7666 (t80) REVERT: D 102 SER cc_start: 0.9216 (t) cc_final: 0.8934 (p) REVERT: D 148 GLU cc_start: 0.8721 (tt0) cc_final: 0.8449 (tt0) REVERT: D 324 MET cc_start: 0.9061 (mtp) cc_final: 0.8391 (ttm) REVERT: D 404 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8447 (tp30) REVERT: D 409 LEU cc_start: 0.9340 (tp) cc_final: 0.8844 (mp) REVERT: E 1 MET cc_start: 0.8911 (tmm) cc_final: 0.8703 (tpt) REVERT: E 22 LEU cc_start: 0.9217 (mt) cc_final: 0.8920 (tp) REVERT: E 69 LEU cc_start: 0.9033 (mt) cc_final: 0.8563 (tt) REVERT: E 78 LYS cc_start: 0.9420 (mmtt) cc_final: 0.8864 (tppt) REVERT: E 82 GLU cc_start: 0.9609 (mt-10) cc_final: 0.9135 (mm-30) REVERT: E 98 VAL cc_start: 0.9536 (OUTLIER) cc_final: 0.8681 (t) REVERT: E 228 ASN cc_start: 0.9663 (t0) cc_final: 0.9328 (p0) REVERT: E 402 ASN cc_start: 0.9515 (m110) cc_final: 0.9090 (p0) REVERT: E 403 LEU cc_start: 0.8220 (mt) cc_final: 0.7901 (mp) REVERT: E 413 LEU cc_start: 0.8547 (mp) cc_final: 0.8342 (mp) REVERT: E 415 LEU cc_start: 0.8634 (mm) cc_final: 0.8429 (mm) REVERT: A 552 LEU cc_start: 0.9387 (tp) cc_final: 0.8979 (pp) REVERT: A 622 ASN cc_start: 0.9261 (t0) cc_final: 0.9041 (p0) REVERT: A 635 MET cc_start: 0.8695 (mmm) cc_final: 0.8338 (mmt) REVERT: B 342 LYS cc_start: 0.9514 (tptt) cc_final: 0.9308 (tppt) REVERT: B 382 ASN cc_start: 0.7785 (m110) cc_final: 0.6793 (p0) REVERT: B 388 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.6987 (mt) REVERT: B 393 MET cc_start: 0.8488 (mpp) cc_final: 0.7820 (pmm) REVERT: B 488 TRP cc_start: 0.8489 (m100) cc_final: 0.8072 (m100) REVERT: C 51 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8801 (mp0) REVERT: C 185 MET cc_start: 0.8929 (mmm) cc_final: 0.8206 (tmm) REVERT: C 189 LYS cc_start: 0.9724 (tttm) cc_final: 0.9514 (tptp) REVERT: C 221 GLN cc_start: 0.9657 (mt0) cc_final: 0.9314 (mp10) REVERT: C 326 PHE cc_start: 0.8172 (m-80) cc_final: 0.7778 (t80) REVERT: C 425 LEU cc_start: 0.9284 (mp) cc_final: 0.9053 (tp) REVERT: C 450 MET cc_start: 0.8736 (ptp) cc_final: 0.8467 (ptp) REVERT: C 625 MET cc_start: 0.7323 (mmt) cc_final: 0.6812 (tpt) outliers start: 33 outliers final: 19 residues processed: 222 average time/residue: 0.2554 time to fit residues: 85.9902 Evaluate side-chains 203 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 153 optimal weight: 8.9990 chunk 124 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.1980 chunk 161 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15433 Z= 0.148 Angle : 0.620 11.007 20882 Z= 0.295 Chirality : 0.041 0.362 2416 Planarity : 0.003 0.043 2642 Dihedral : 7.498 72.702 2146 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.88 % Allowed : 16.75 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.44 (0.20), residues: 1843 helix: 0.95 (0.16), residues: 1116 sheet: -1.41 (0.36), residues: 161 loop : -0.29 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 475 HIS 0.008 0.001 HIS B 362 PHE 0.017 0.001 PHE C 332 TYR 0.015 0.001 TYR C 255 ARG 0.004 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8458 (t80) cc_final: 0.7721 (t80) REVERT: D 102 SER cc_start: 0.9212 (t) cc_final: 0.8944 (p) REVERT: D 148 GLU cc_start: 0.8740 (tt0) cc_final: 0.8461 (tt0) REVERT: D 324 MET cc_start: 0.9045 (mtp) cc_final: 0.8389 (ttm) REVERT: D 404 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8431 (tp30) REVERT: D 409 LEU cc_start: 0.9339 (tp) cc_final: 0.8809 (mp) REVERT: E 22 LEU cc_start: 0.9235 (mt) cc_final: 0.8917 (tp) REVERT: E 69 LEU cc_start: 0.8998 (mt) cc_final: 0.8610 (tt) REVERT: E 78 LYS cc_start: 0.9395 (mmtt) cc_final: 0.8754 (tppt) REVERT: E 80 MET cc_start: 0.9703 (ttm) cc_final: 0.9443 (mtt) REVERT: E 82 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9075 (mm-30) REVERT: E 98 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.8084 (t) REVERT: E 106 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9300 (mm-30) REVERT: E 228 ASN cc_start: 0.9655 (t0) cc_final: 0.9330 (p0) REVERT: E 402 ASN cc_start: 0.9528 (m110) cc_final: 0.9075 (p0) REVERT: E 403 LEU cc_start: 0.8224 (mt) cc_final: 0.7868 (mp) REVERT: E 415 LEU cc_start: 0.8622 (mm) cc_final: 0.8399 (mm) REVERT: A 552 LEU cc_start: 0.9378 (tp) cc_final: 0.8916 (pp) REVERT: A 630 LEU cc_start: 0.9247 (mm) cc_final: 0.8911 (mm) REVERT: A 635 MET cc_start: 0.8721 (mmm) cc_final: 0.7954 (mmt) REVERT: A 855 MET cc_start: 0.8795 (ppp) cc_final: 0.8361 (ppp) REVERT: B 342 LYS cc_start: 0.9513 (tptt) cc_final: 0.9143 (tppt) REVERT: B 388 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7205 (mt) REVERT: B 393 MET cc_start: 0.8498 (mpp) cc_final: 0.7903 (pmm) REVERT: B 488 TRP cc_start: 0.8519 (m100) cc_final: 0.7907 (m100) REVERT: C 51 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8787 (mp0) REVERT: C 189 LYS cc_start: 0.9719 (tttm) cc_final: 0.9514 (tptp) REVERT: C 326 PHE cc_start: 0.8239 (m-80) cc_final: 0.7899 (t80) REVERT: C 425 LEU cc_start: 0.9268 (mp) cc_final: 0.8999 (tp) REVERT: C 429 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9150 (mp) REVERT: C 504 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7975 (pp20) REVERT: C 625 MET cc_start: 0.7304 (mmt) cc_final: 0.6812 (tpt) outliers start: 31 outliers final: 18 residues processed: 218 average time/residue: 0.2524 time to fit residues: 83.4439 Evaluate side-chains 199 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15433 Z= 0.192 Angle : 0.629 11.329 20882 Z= 0.301 Chirality : 0.040 0.284 2416 Planarity : 0.003 0.039 2642 Dihedral : 7.429 79.870 2146 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.49 % Allowed : 16.87 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.55 (0.20), residues: 1843 helix: 1.02 (0.16), residues: 1126 sheet: -1.30 (0.37), residues: 161 loop : -0.26 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 475 HIS 0.006 0.001 HIS B 362 PHE 0.020 0.001 PHE C 332 TYR 0.023 0.001 TYR A 579 ARG 0.004 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 1.715 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: D 77 LYS cc_start: 0.9461 (mttt) cc_final: 0.9243 (mmtt) REVERT: D 79 PHE cc_start: 0.8484 (t80) cc_final: 0.7755 (t80) REVERT: D 102 SER cc_start: 0.9239 (t) cc_final: 0.8963 (p) REVERT: D 148 GLU cc_start: 0.8690 (tt0) cc_final: 0.8398 (tt0) REVERT: D 324 MET cc_start: 0.9145 (mtp) cc_final: 0.8491 (ttm) REVERT: D 404 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8630 (tp30) REVERT: D 407 MET cc_start: 0.8482 (ptm) cc_final: 0.8154 (ppp) REVERT: E 22 LEU cc_start: 0.9212 (mt) cc_final: 0.8948 (tp) REVERT: E 80 MET cc_start: 0.9709 (ttm) cc_final: 0.9455 (mtt) REVERT: E 82 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9162 (mm-30) REVERT: E 98 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.8593 (t) REVERT: E 226 TYR cc_start: 0.9021 (t80) cc_final: 0.8800 (t80) REVERT: E 228 ASN cc_start: 0.9675 (t0) cc_final: 0.9341 (p0) REVERT: E 402 ASN cc_start: 0.9510 (m110) cc_final: 0.8957 (p0) REVERT: E 403 LEU cc_start: 0.8247 (mt) cc_final: 0.7896 (mp) REVERT: A 552 LEU cc_start: 0.9310 (tp) cc_final: 0.8897 (pp) REVERT: A 635 MET cc_start: 0.8748 (mmm) cc_final: 0.8413 (mmt) REVERT: A 701 LEU cc_start: 0.8855 (tp) cc_final: 0.8580 (pp) REVERT: A 853 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 855 MET cc_start: 0.8750 (ppp) cc_final: 0.8125 (ppp) REVERT: B 342 LYS cc_start: 0.9431 (tptt) cc_final: 0.9225 (tppt) REVERT: B 388 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7384 (mt) REVERT: B 488 TRP cc_start: 0.8473 (m100) cc_final: 0.7890 (m100) REVERT: C 51 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8777 (mp0) REVERT: C 326 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7980 (t80) REVERT: C 388 LYS cc_start: 0.9242 (tptp) cc_final: 0.9012 (tptp) REVERT: C 425 LEU cc_start: 0.9274 (mp) cc_final: 0.8982 (tp) REVERT: C 429 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9167 (mp) REVERT: C 450 MET cc_start: 0.8832 (ptp) cc_final: 0.8577 (ptp) REVERT: C 504 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7972 (pp20) REVERT: C 625 MET cc_start: 0.7244 (mmt) cc_final: 0.6799 (tpt) outliers start: 41 outliers final: 27 residues processed: 202 average time/residue: 0.2534 time to fit residues: 78.6222 Evaluate side-chains 203 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 504 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15433 Z= 0.174 Angle : 0.651 12.619 20882 Z= 0.305 Chirality : 0.040 0.297 2416 Planarity : 0.004 0.118 2642 Dihedral : 7.397 89.262 2146 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.31 % Allowed : 17.35 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.68 (0.20), residues: 1843 helix: 1.10 (0.16), residues: 1123 sheet: -1.17 (0.37), residues: 167 loop : -0.17 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 475 HIS 0.005 0.001 HIS B 362 PHE 0.015 0.001 PHE C 332 TYR 0.010 0.001 TYR C 430 ARG 0.009 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.944 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: D 77 LYS cc_start: 0.9469 (mttt) cc_final: 0.9259 (mmtt) REVERT: D 79 PHE cc_start: 0.8449 (t80) cc_final: 0.7743 (t80) REVERT: D 102 SER cc_start: 0.9260 (t) cc_final: 0.8979 (p) REVERT: D 148 GLU cc_start: 0.8677 (tt0) cc_final: 0.8389 (tt0) REVERT: D 324 MET cc_start: 0.9130 (mtp) cc_final: 0.8476 (ttm) REVERT: D 404 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8668 (tp30) REVERT: E 22 LEU cc_start: 0.9209 (mt) cc_final: 0.8953 (tp) REVERT: E 69 LEU cc_start: 0.8918 (mm) cc_final: 0.8571 (tt) REVERT: E 78 LYS cc_start: 0.9423 (mmtt) cc_final: 0.8759 (tppt) REVERT: E 80 MET cc_start: 0.9706 (ttm) cc_final: 0.9490 (mtt) REVERT: E 82 GLU cc_start: 0.9592 (mt-10) cc_final: 0.9056 (mm-30) REVERT: E 98 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.7867 (t) REVERT: E 106 GLU cc_start: 0.9535 (OUTLIER) cc_final: 0.9323 (mm-30) REVERT: E 226 TYR cc_start: 0.9013 (t80) cc_final: 0.8744 (t80) REVERT: E 228 ASN cc_start: 0.9672 (t0) cc_final: 0.9336 (p0) REVERT: E 402 ASN cc_start: 0.9484 (m110) cc_final: 0.9017 (p0) REVERT: A 552 LEU cc_start: 0.9275 (tp) cc_final: 0.8915 (pp) REVERT: A 630 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9003 (mm) REVERT: A 635 MET cc_start: 0.8769 (mmm) cc_final: 0.8436 (mmt) REVERT: A 701 LEU cc_start: 0.8843 (tp) cc_final: 0.8584 (pp) REVERT: A 767 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9172 (tp30) REVERT: A 853 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 855 MET cc_start: 0.8775 (ppp) cc_final: 0.8156 (ppp) REVERT: B 388 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7158 (mt) REVERT: B 393 MET cc_start: 0.8611 (mpp) cc_final: 0.8081 (pmm) REVERT: B 488 TRP cc_start: 0.8439 (m100) cc_final: 0.7827 (m100) REVERT: C 51 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8793 (mp0) REVERT: C 326 PHE cc_start: 0.8336 (m-80) cc_final: 0.7997 (t80) REVERT: C 388 LYS cc_start: 0.9244 (tptp) cc_final: 0.9001 (tptp) REVERT: C 425 LEU cc_start: 0.9259 (mp) cc_final: 0.8976 (tp) REVERT: C 429 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9167 (mp) REVERT: C 504 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7973 (pp20) REVERT: C 625 MET cc_start: 0.7231 (mmt) cc_final: 0.6870 (tpt) outliers start: 38 outliers final: 28 residues processed: 200 average time/residue: 0.2636 time to fit residues: 79.9883 Evaluate side-chains 206 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 0.0030 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 overall best weight: 3.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 243 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15433 Z= 0.246 Angle : 0.680 11.259 20882 Z= 0.328 Chirality : 0.040 0.256 2416 Planarity : 0.003 0.038 2642 Dihedral : 7.517 78.416 2146 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.73 % Allowed : 18.20 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.74 (0.20), residues: 1843 helix: 1.12 (0.16), residues: 1126 sheet: -1.02 (0.38), residues: 167 loop : -0.11 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 475 HIS 0.006 0.001 HIS D 427 PHE 0.026 0.002 PHE C 332 TYR 0.026 0.002 TYR A 579 ARG 0.005 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 1.938 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: D 77 LYS cc_start: 0.9481 (mttt) cc_final: 0.9248 (mmtt) REVERT: D 79 PHE cc_start: 0.8499 (t80) cc_final: 0.7797 (t80) REVERT: D 148 GLU cc_start: 0.8582 (tt0) cc_final: 0.8300 (tt0) REVERT: D 149 PHE cc_start: 0.8364 (t80) cc_final: 0.8128 (t80) REVERT: D 404 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8882 (tp30) REVERT: D 407 MET cc_start: 0.8515 (ppp) cc_final: 0.8243 (ppp) REVERT: E 78 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8746 (tppt) REVERT: E 80 MET cc_start: 0.9690 (ttm) cc_final: 0.9468 (mtt) REVERT: E 82 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9244 (mt-10) REVERT: E 98 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9164 (t) REVERT: E 228 ASN cc_start: 0.9700 (t0) cc_final: 0.9298 (p0) REVERT: E 402 ASN cc_start: 0.9514 (m110) cc_final: 0.8827 (t0) REVERT: E 406 GLN cc_start: 0.8592 (mm110) cc_final: 0.8084 (mm110) REVERT: A 552 LEU cc_start: 0.9296 (tp) cc_final: 0.8924 (pp) REVERT: A 630 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 635 MET cc_start: 0.8800 (mmm) cc_final: 0.8509 (mmt) REVERT: A 697 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9090 (m) REVERT: A 701 LEU cc_start: 0.8820 (tp) cc_final: 0.8607 (pp) REVERT: A 767 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9138 (tp30) REVERT: A 853 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8752 (t) REVERT: A 855 MET cc_start: 0.8817 (ppp) cc_final: 0.8214 (ppp) REVERT: B 342 LYS cc_start: 0.9398 (tptt) cc_final: 0.9038 (tppt) REVERT: B 382 ASN cc_start: 0.7919 (m110) cc_final: 0.6867 (p0) REVERT: B 388 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7255 (mt) REVERT: B 393 MET cc_start: 0.8691 (mpp) cc_final: 0.8210 (pmm) REVERT: B 488 TRP cc_start: 0.8382 (m100) cc_final: 0.7735 (m100) REVERT: C 51 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8904 (mp0) REVERT: C 326 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8163 (t80) REVERT: C 327 PHE cc_start: 0.7001 (m-80) cc_final: 0.6524 (m-10) REVERT: C 344 ARG cc_start: 0.9729 (mmt180) cc_final: 0.9160 (mmp80) REVERT: C 388 LYS cc_start: 0.9250 (tptp) cc_final: 0.8996 (tptp) REVERT: C 425 LEU cc_start: 0.9248 (mp) cc_final: 0.8978 (tp) REVERT: C 429 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9189 (mp) REVERT: C 430 TYR cc_start: 0.9142 (t80) cc_final: 0.8853 (t80) REVERT: C 625 MET cc_start: 0.7226 (mmt) cc_final: 0.6901 (tpt) outliers start: 45 outliers final: 33 residues processed: 195 average time/residue: 0.2587 time to fit residues: 77.4613 Evaluate side-chains 202 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15433 Z= 0.237 Angle : 0.681 11.517 20882 Z= 0.326 Chirality : 0.040 0.268 2416 Planarity : 0.003 0.055 2642 Dihedral : 7.589 77.036 2146 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.37 % Allowed : 18.99 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.84 (0.20), residues: 1843 helix: 1.17 (0.16), residues: 1131 sheet: -0.98 (0.39), residues: 167 loop : -0.02 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 475 HIS 0.008 0.001 HIS C 250 PHE 0.025 0.002 PHE D 206 TYR 0.015 0.001 TYR E 291 ARG 0.008 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8598 (tt0) cc_final: 0.8319 (tt0) REVERT: D 404 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8934 (tp30) REVERT: D 407 MET cc_start: 0.8533 (ppp) cc_final: 0.8266 (ppp) REVERT: E 78 LYS cc_start: 0.9407 (mmtt) cc_final: 0.8878 (tppt) REVERT: E 80 MET cc_start: 0.9709 (ttm) cc_final: 0.9495 (mtt) REVERT: E 82 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9298 (mt-10) REVERT: E 226 TYR cc_start: 0.9044 (t80) cc_final: 0.8694 (t80) REVERT: E 228 ASN cc_start: 0.9716 (t0) cc_final: 0.9323 (p0) REVERT: E 292 MET cc_start: 0.7556 (mmm) cc_final: 0.7331 (mmm) REVERT: A 552 LEU cc_start: 0.9298 (tp) cc_final: 0.8920 (pp) REVERT: A 630 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8877 (mm) REVERT: A 635 MET cc_start: 0.8804 (mmm) cc_final: 0.8519 (mmt) REVERT: A 701 LEU cc_start: 0.8819 (tp) cc_final: 0.8607 (pp) REVERT: A 853 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8752 (t) REVERT: A 855 MET cc_start: 0.8808 (ppp) cc_final: 0.8202 (ppp) REVERT: B 388 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7363 (mt) REVERT: B 393 MET cc_start: 0.8712 (mpp) cc_final: 0.8203 (pmm) REVERT: B 488 TRP cc_start: 0.8371 (m100) cc_final: 0.7646 (m100) REVERT: C 326 PHE cc_start: 0.8516 (m-80) cc_final: 0.8163 (t80) REVERT: C 327 PHE cc_start: 0.7066 (m-80) cc_final: 0.6722 (m-10) REVERT: C 344 ARG cc_start: 0.9723 (mmt180) cc_final: 0.9150 (mmp80) REVERT: C 425 LEU cc_start: 0.9208 (mp) cc_final: 0.8935 (tp) REVERT: C 429 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9209 (mp) REVERT: C 430 TYR cc_start: 0.9128 (t80) cc_final: 0.8843 (t80) REVERT: C 625 MET cc_start: 0.7219 (mmt) cc_final: 0.6905 (tpt) outliers start: 39 outliers final: 31 residues processed: 188 average time/residue: 0.2521 time to fit residues: 72.9776 Evaluate side-chains 194 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN E 107 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15433 Z= 0.177 Angle : 0.667 12.148 20882 Z= 0.313 Chirality : 0.040 0.300 2416 Planarity : 0.003 0.038 2642 Dihedral : 7.508 78.340 2146 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.82 % Allowed : 19.72 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.94 (0.20), residues: 1843 helix: 1.26 (0.16), residues: 1128 sheet: -0.88 (0.39), residues: 167 loop : -0.02 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.004 0.001 HIS A 809 PHE 0.019 0.001 PHE C 332 TYR 0.034 0.001 TYR E 291 ARG 0.005 0.000 ARG F 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.839 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: D 79 PHE cc_start: 0.8476 (t80) cc_final: 0.7795 (t80) REVERT: D 148 GLU cc_start: 0.8599 (tt0) cc_final: 0.8322 (tt0) REVERT: D 149 PHE cc_start: 0.8336 (t80) cc_final: 0.8082 (t80) REVERT: D 404 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8843 (tp30) REVERT: D 407 MET cc_start: 0.8536 (ppp) cc_final: 0.8273 (ppp) REVERT: E 78 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9082 (mmmm) REVERT: E 82 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9361 (mt-10) REVERT: E 88 LEU cc_start: 0.8943 (mm) cc_final: 0.8708 (mm) REVERT: E 226 TYR cc_start: 0.9041 (t80) cc_final: 0.8669 (t80) REVERT: E 228 ASN cc_start: 0.9703 (t0) cc_final: 0.9310 (p0) REVERT: E 292 MET cc_start: 0.7560 (mmm) cc_final: 0.7337 (mmm) REVERT: A 552 LEU cc_start: 0.9264 (tp) cc_final: 0.8913 (pp) REVERT: A 630 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 635 MET cc_start: 0.8839 (mmm) cc_final: 0.8272 (mmt) REVERT: A 701 LEU cc_start: 0.8802 (tp) cc_final: 0.8578 (pp) REVERT: A 853 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8738 (t) REVERT: A 855 MET cc_start: 0.8804 (ppp) cc_final: 0.8186 (ppp) REVERT: B 388 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7323 (mt) REVERT: B 393 MET cc_start: 0.8716 (mpp) cc_final: 0.8202 (pmm) REVERT: B 488 TRP cc_start: 0.8402 (m100) cc_final: 0.7666 (m100) REVERT: C 223 LEU cc_start: 0.9831 (tt) cc_final: 0.9565 (mp) REVERT: C 326 PHE cc_start: 0.8530 (m-80) cc_final: 0.8195 (t80) REVERT: C 344 ARG cc_start: 0.9667 (mmt180) cc_final: 0.9319 (mmt90) REVERT: C 425 LEU cc_start: 0.9171 (mp) cc_final: 0.8883 (tp) REVERT: C 429 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9231 (mp) REVERT: C 430 TYR cc_start: 0.9094 (t80) cc_final: 0.8794 (t80) REVERT: C 625 MET cc_start: 0.7130 (mmt) cc_final: 0.6836 (tpt) outliers start: 30 outliers final: 23 residues processed: 186 average time/residue: 0.2598 time to fit residues: 74.2103 Evaluate side-chains 186 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045338 restraints weight = 90549.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.046896 restraints weight = 51482.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047945 restraints weight = 34844.369| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15433 Z= 0.222 Angle : 0.698 15.821 20882 Z= 0.331 Chirality : 0.041 0.302 2416 Planarity : 0.003 0.039 2642 Dihedral : 7.556 79.223 2146 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 19.60 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.92 (0.20), residues: 1843 helix: 1.23 (0.16), residues: 1128 sheet: -0.85 (0.39), residues: 167 loop : -0.00 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 475 HIS 0.004 0.001 HIS C 230 PHE 0.024 0.002 PHE A 581 TYR 0.045 0.001 TYR E 291 ARG 0.005 0.000 ARG F 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.80 seconds wall clock time: 53 minutes 39.12 seconds (3219.12 seconds total)