Starting phenix.real_space_refine on Mon Apr 8 14:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz0_20585/04_2024/6tz0_20585.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8708 2.51 5 N 2333 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A ARG 1146": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 520": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13674 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Time building chain proxies: 7.40, per 1000 atoms: 0.54 Number of scatterers: 13674 At special positions: 0 Unit cell: (105.138, 145.494, 84.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2579 8.00 N 2333 7.00 C 8708 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=0, symmetry=0 Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 17 sheets defined 50.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.702A pdb=" N GLU A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 4.209A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.583A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.745A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.662A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.066A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.811A pdb=" N GLY A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.395A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.690A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 removed outlier: 3.534A pdb=" N SER A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.865A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.880A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.511A pdb=" N TYR A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.143A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.560A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.521A pdb=" N TYR A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 529 through 536 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.610A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 643 through 666 removed outlier: 3.779A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.564A pdb=" N ARG A 738 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 739' Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.557A pdb=" N MET A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.692A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.542A pdb=" N THR A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.700A pdb=" N MET A 839 " --> pdb=" O TRP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 4.045A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 901 through 912 removed outlier: 3.666A pdb=" N ALA A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 926 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 944 through 959 removed outlier: 3.824A pdb=" N LYS A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 995 through 1005 removed outlier: 4.115A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.947A pdb=" N ALA A1018 " --> pdb=" O PRO A1015 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A1020 " --> pdb=" O ASP A1017 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1015 through 1020' Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.601A pdb=" N LYS A1038 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1073 through 1081 removed outlier: 3.802A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1117 through 1133 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1173 through 1189 removed outlier: 3.843A pdb=" N LEU A1177 " --> pdb=" O GLN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.669A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.638A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.648A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.766A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.063A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 325 through 341 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.737A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.999A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.542A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.655A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.742A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.613A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 538 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.708A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.645A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.581A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.758A pdb=" N SER A 380 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A 374 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 437 removed outlier: 6.155A pdb=" N GLU A 434 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP A 445 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 436 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 removed outlier: 5.741A pdb=" N ILE A 474 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU A 623 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU A 476 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 677 removed outlier: 7.084A pdb=" N ILE A 685 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 675 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET A 683 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA9, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.985A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 791 through 795 removed outlier: 3.507A pdb=" N ILE A 831 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AB3, first strand: chain 'A' and resid 919 through 921 Processing sheet with id=AB4, first strand: chain 'A' and resid 1022 through 1030 removed outlier: 4.287A pdb=" N ARG A1197 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.959A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 204 through 208 removed outlier: 6.214A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 297 through 299 removed outlier: 3.503A pdb=" N VAL B 267 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 255 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.618A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 353 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR B 504 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1653 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: 4.81 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3588 1.33 - 1.45: 2659 1.45 - 1.57: 7625 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 13968 Sorted by residual: bond pdb=" CB VAL A 589 " pdb=" CG2 VAL A 589 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.02e+00 bond pdb=" CB PHE A 206 " pdb=" CG PHE A 206 " ideal model delta sigma weight residual 1.502 1.464 0.038 2.30e-02 1.89e+03 2.80e+00 bond pdb=" N VAL A 891 " pdb=" CA VAL A 891 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.15e-02 7.56e+03 2.53e+00 bond pdb=" CA VAL A 891 " pdb=" C VAL A 891 " ideal model delta sigma weight residual 1.525 1.508 0.017 1.17e-02 7.31e+03 2.17e+00 bond pdb=" CA ASP A 893 " pdb=" C ASP A 893 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.35e-02 5.49e+03 2.11e+00 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.20: 214 105.20 - 112.41: 6789 112.41 - 119.63: 4980 119.63 - 126.84: 6786 126.84 - 134.06: 149 Bond angle restraints: 18918 Sorted by residual: angle pdb=" N CYS A 788 " pdb=" CA CYS A 788 " pdb=" C CYS A 788 " ideal model delta sigma weight residual 111.36 118.61 -7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" N ARG A 790 " pdb=" CA ARG A 790 " pdb=" C ARG A 790 " ideal model delta sigma weight residual 113.16 120.08 -6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ARG A 791 " pdb=" CA ARG A 791 " pdb=" C ARG A 791 " ideal model delta sigma weight residual 109.07 117.13 -8.06 1.61e+00 3.86e-01 2.50e+01 angle pdb=" C GLY A 427 " pdb=" N ARG A 428 " pdb=" CA ARG A 428 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+01 angle pdb=" N LEU A 892 " pdb=" CA LEU A 892 " pdb=" C LEU A 892 " ideal model delta sigma weight residual 110.28 103.27 7.01 1.48e+00 4.57e-01 2.24e+01 ... (remaining 18913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 7822 14.15 - 28.30: 416 28.30 - 42.46: 121 42.46 - 56.61: 15 56.61 - 70.76: 6 Dihedral angle restraints: 8380 sinusoidal: 3348 harmonic: 5032 Sorted by residual: dihedral pdb=" CA GLN A 480 " pdb=" C GLN A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A 753 " pdb=" C LEU A 753 " pdb=" N ASN A 754 " pdb=" CA ASN A 754 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N GLN A 363 " pdb=" C GLN A 363 " pdb=" CA GLN A 363 " pdb=" CB GLN A 363 " ideal model delta harmonic sigma weight residual 122.80 133.83 -11.03 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1903 0.094 - 0.188: 195 0.188 - 0.281: 10 0.281 - 0.375: 3 0.375 - 0.469: 1 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA GLN A 363 " pdb=" N GLN A 363 " pdb=" C GLN A 363 " pdb=" CB GLN A 363 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL A 771 " pdb=" CA VAL A 771 " pdb=" CG1 VAL A 771 " pdb=" CG2 VAL A 771 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2109 not shown) Planarity restraints: 2417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.028 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 606 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " -0.018 2.00e-02 2.50e+03 2.37e-02 9.87e+00 pdb=" CG PHE A 769 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 203 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 204 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.041 5.00e-02 4.00e+02 ... (remaining 2414 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4083 2.82 - 3.34: 11899 3.34 - 3.86: 22703 3.86 - 4.38: 26743 4.38 - 4.90: 45779 Nonbonded interactions: 111207 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR B 386 " pdb=" O HIS B 466 " model vdw 2.301 2.440 nonbonded pdb=" O LYS A 778 " pdb=" OH TYR A 845 " model vdw 2.312 2.440 nonbonded pdb=" OG SER A 716 " pdb=" O SER A 719 " model vdw 2.312 2.440 nonbonded pdb=" OE2 GLU A 612 " pdb=" NH2 ARG A 641 " model vdw 2.318 2.520 ... (remaining 111202 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 individual isotropic 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: 1.060 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: 4.390 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13968 Z= 0.417 Angle : 0.939 9.650 18918 Z= 0.509 Chirality : 0.058 0.469 2112 Planarity : 0.007 0.072 2417 Dihedral : 10.042 70.759 5146 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.54 % Allowed : 3.56 % Favored : 95.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.16), residues: 1701 helix: -2.41 (0.13), residues: 810 sheet: -1.18 (0.34), residues: 176 loop : -1.97 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP A 606 HIS 0.018 0.003 HIS B 59 PHE 0.054 0.004 PHE A 769 TYR 0.040 0.003 TYR A 331 ARG 0.016 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 405 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 203 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8696 (tt) REVERT: A 906 LEU cc_start: 0.8827 (mt) cc_final: 0.8458 (mt) REVERT: A 988 THR cc_start: 0.7797 (p) cc_final: 0.7362 (m) REVERT: A 998 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 1019 LEU cc_start: 0.8713 (mt) cc_final: 0.8451 (mt) REVERT: A 1022 TYR cc_start: 0.8654 (p90) cc_final: 0.8133 (p90) REVERT: A 1080 ARG cc_start: 0.6767 (tmt90) cc_final: 0.6537 (ttt180) REVERT: A 1098 LYS cc_start: 0.8339 (mttm) cc_final: 0.7797 (pttt) REVERT: A 1126 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7235 (mtt90) REVERT: A 1133 LEU cc_start: 0.7447 (mt) cc_final: 0.7197 (pp) REVERT: B 450 ASP cc_start: 0.8295 (m-30) cc_final: 0.7820 (m-30) outliers start: 8 outliers final: 3 residues processed: 409 average time/residue: 1.5258 time to fit residues: 673.9234 Evaluate side-chains 241 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 427 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 0.0470 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 236 HIS A 375 ASN A 378 HIS A 412 HIS A 481 GLN A 629 GLN A 717 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN A 931 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS A1095 GLN A1121 GLN A1140 HIS A1194 GLN B 180 GLN B 212 ASN B 217 GLN B 272 ASN B 436 GLN B 459 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.217 Angle : 0.563 7.212 18918 Z= 0.297 Chirality : 0.042 0.178 2112 Planarity : 0.004 0.042 2417 Dihedral : 5.407 54.368 1905 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 3.36 % Allowed : 12.03 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 1701 helix: -0.53 (0.17), residues: 811 sheet: -0.76 (0.36), residues: 172 loop : -1.35 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 606 HIS 0.008 0.002 HIS B 59 PHE 0.024 0.002 PHE A 769 TYR 0.023 0.002 TYR B 253 ARG 0.007 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8793 (mttp) REVERT: A 231 MET cc_start: 0.8439 (mmm) cc_final: 0.8193 (mmp) REVERT: A 302 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7996 (mtmm) REVERT: A 481 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: A 752 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6562 (mpt-90) REVERT: A 942 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7956 (tppp) REVERT: A 978 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6996 (tp40) REVERT: A 988 THR cc_start: 0.7751 (p) cc_final: 0.7442 (m) REVERT: A 1080 ARG cc_start: 0.6787 (tmt90) cc_final: 0.6464 (ttt180) REVERT: A 1098 LYS cc_start: 0.8327 (mttm) cc_final: 0.7822 (pttt) REVERT: A 1107 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7092 (tm) REVERT: A 1126 ARG cc_start: 0.7760 (mtp180) cc_final: 0.7186 (mtt90) REVERT: B 136 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8183 (ptmt) REVERT: B 254 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: B 419 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: B 450 ASP cc_start: 0.8351 (m-30) cc_final: 0.8029 (m-30) outliers start: 50 outliers final: 20 residues processed: 296 average time/residue: 1.5596 time to fit residues: 497.4039 Evaluate side-chains 243 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.1980 chunk 47 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 375 ASN A 481 GLN A 514 ASN A 629 GLN A 653 GLN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 212 ASN B 429 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13968 Z= 0.135 Angle : 0.492 8.190 18918 Z= 0.257 Chirality : 0.039 0.182 2112 Planarity : 0.003 0.034 2417 Dihedral : 4.490 44.568 1899 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.90 % Allowed : 13.51 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1701 helix: 0.40 (0.18), residues: 813 sheet: -0.64 (0.36), residues: 170 loop : -1.08 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 606 HIS 0.004 0.001 HIS A 126 PHE 0.013 0.001 PHE A 769 TYR 0.014 0.001 TYR B 253 ARG 0.006 0.000 ARG A1073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8671 (mttp) REVERT: A 37 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6927 (ptm-80) REVERT: A 100 LYS cc_start: 0.8502 (mptp) cc_final: 0.8251 (mppt) REVERT: A 302 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8067 (mtmm) REVERT: A 481 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: A 771 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 978 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6988 (tp40) REVERT: A 988 THR cc_start: 0.7717 (p) cc_final: 0.7448 (m) REVERT: A 1080 ARG cc_start: 0.6708 (tmt90) cc_final: 0.6430 (ttt180) REVERT: A 1098 LYS cc_start: 0.8257 (mttm) cc_final: 0.7729 (pttt) REVERT: A 1107 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7088 (tm) REVERT: A 1126 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7145 (mtt90) REVERT: B 419 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7618 (mt-10) outliers start: 58 outliers final: 23 residues processed: 274 average time/residue: 1.6620 time to fit residues: 491.3789 Evaluate side-chains 235 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 481 GLN A 687 GLN A 717 GLN A 887 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 212 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13968 Z= 0.223 Angle : 0.535 8.089 18918 Z= 0.279 Chirality : 0.041 0.189 2112 Planarity : 0.004 0.033 2417 Dihedral : 4.529 46.651 1897 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.44 % Allowed : 13.64 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1701 helix: 0.79 (0.18), residues: 809 sheet: -0.65 (0.37), residues: 170 loop : -0.95 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 606 HIS 0.007 0.001 HIS B 59 PHE 0.016 0.002 PHE A 769 TYR 0.018 0.002 TYR B 253 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 218 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8800 (mttp) REVERT: A 37 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7009 (ptm-80) REVERT: A 218 MET cc_start: 0.8633 (mmm) cc_final: 0.8405 (mmp) REVERT: A 481 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: A 771 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8076 (m) REVERT: A 794 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8284 (pp) REVERT: A 906 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 978 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: A 988 THR cc_start: 0.7624 (p) cc_final: 0.7316 (m) REVERT: A 992 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6987 (mmtp) REVERT: A 1098 LYS cc_start: 0.8264 (mttm) cc_final: 0.7730 (pttt) REVERT: A 1107 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7099 (tm) REVERT: A 1126 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7261 (mtt90) REVERT: B 254 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: B 419 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7683 (mt-10) outliers start: 66 outliers final: 38 residues processed: 261 average time/residue: 1.5739 time to fit residues: 442.7952 Evaluate side-chains 251 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 481 GLN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13968 Z= 0.242 Angle : 0.543 8.384 18918 Z= 0.284 Chirality : 0.042 0.198 2112 Planarity : 0.004 0.034 2417 Dihedral : 4.590 48.496 1897 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.37 % Allowed : 14.38 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1701 helix: 0.88 (0.18), residues: 818 sheet: -0.55 (0.38), residues: 170 loop : -0.92 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 606 HIS 0.008 0.001 HIS B 59 PHE 0.016 0.002 PHE A 206 TYR 0.018 0.002 TYR A 511 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 1.716 Fit side-chains REVERT: A 17 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8848 (mttp) REVERT: A 37 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7121 (ptm-80) REVERT: A 752 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6687 (tpt-90) REVERT: A 771 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8165 (m) REVERT: A 794 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8277 (pp) REVERT: A 906 LEU cc_start: 0.8844 (mp) cc_final: 0.8570 (mt) REVERT: A 959 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7456 (tpp-160) REVERT: A 978 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: A 988 THR cc_start: 0.7632 (p) cc_final: 0.7306 (m) REVERT: A 992 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7135 (mmtp) REVERT: A 1098 LYS cc_start: 0.8275 (mttm) cc_final: 0.7763 (pttt) REVERT: A 1107 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7159 (tm) REVERT: A 1126 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7284 (mtt90) REVERT: B 254 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: B 419 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7704 (mt-10) outliers start: 65 outliers final: 37 residues processed: 257 average time/residue: 1.5661 time to fit residues: 433.7792 Evaluate side-chains 252 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 617 GLN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13968 Z= 0.272 Angle : 0.559 9.159 18918 Z= 0.292 Chirality : 0.042 0.211 2112 Planarity : 0.004 0.036 2417 Dihedral : 4.660 50.052 1897 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.44 % Allowed : 14.92 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1701 helix: 1.04 (0.18), residues: 802 sheet: -0.53 (0.38), residues: 172 loop : -0.79 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 606 HIS 0.009 0.001 HIS B 59 PHE 0.017 0.002 PHE A 206 TYR 0.019 0.002 TYR A 511 ARG 0.007 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 209 time to evaluate : 1.768 Fit side-chains REVERT: A 17 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8885 (mttp) REVERT: A 37 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7166 (ptm-80) REVERT: A 484 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6827 (mpp80) REVERT: A 752 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6704 (tpt-90) REVERT: A 906 LEU cc_start: 0.8831 (mp) cc_final: 0.8577 (mt) REVERT: A 978 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7070 (tp40) REVERT: A 988 THR cc_start: 0.7661 (p) cc_final: 0.7322 (m) REVERT: A 1098 LYS cc_start: 0.8252 (mttm) cc_final: 0.7753 (pttt) REVERT: A 1107 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7167 (tm) REVERT: A 1126 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7270 (mtt90) REVERT: B 254 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: B 419 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7700 (mt-10) outliers start: 66 outliers final: 40 residues processed: 253 average time/residue: 1.6047 time to fit residues: 438.2047 Evaluate side-chains 248 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 375 ASN A 514 ASN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN B 346 ASN ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.273 Angle : 0.563 10.664 18918 Z= 0.295 Chirality : 0.043 0.212 2112 Planarity : 0.004 0.038 2417 Dihedral : 4.691 51.691 1897 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.44 % Allowed : 15.32 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1701 helix: 1.08 (0.18), residues: 802 sheet: -0.64 (0.37), residues: 184 loop : -0.78 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 260 HIS 0.008 0.001 HIS B 59 PHE 0.017 0.002 PHE A 206 TYR 0.018 0.002 TYR A 511 ARG 0.007 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 215 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8910 (mttp) REVERT: A 37 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7173 (ptm-80) REVERT: A 116 TYR cc_start: 0.8222 (m-80) cc_final: 0.7999 (m-80) REVERT: A 161 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: A 484 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6819 (mpp80) REVERT: A 752 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6881 (tpt-90) REVERT: A 794 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7982 (pp) REVERT: A 906 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 978 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7079 (tp40) REVERT: A 988 THR cc_start: 0.7736 (p) cc_final: 0.7399 (m) REVERT: A 1098 LYS cc_start: 0.8256 (mttm) cc_final: 0.7757 (pttt) REVERT: A 1107 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7270 (tm) REVERT: A 1126 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7274 (mtt90) REVERT: B 254 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 419 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7710 (mt-10) outliers start: 66 outliers final: 44 residues processed: 255 average time/residue: 1.7008 time to fit residues: 465.9468 Evaluate side-chains 256 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 375 ASN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13968 Z= 0.209 Angle : 0.538 11.367 18918 Z= 0.280 Chirality : 0.041 0.199 2112 Planarity : 0.004 0.037 2417 Dihedral : 4.561 52.712 1897 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.97 % Allowed : 16.47 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1701 helix: 1.26 (0.19), residues: 801 sheet: -0.46 (0.38), residues: 174 loop : -0.75 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.006 0.001 HIS B 59 PHE 0.014 0.001 PHE A 206 TYR 0.014 0.001 TYR A 511 ARG 0.008 0.001 ARG A1073 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8885 (mttp) REVERT: A 37 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7141 (ptm-80) REVERT: A 161 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8146 (mm-40) REVERT: A 484 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6864 (mpp80) REVERT: A 752 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6922 (tpt-90) REVERT: A 771 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 794 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8043 (pp) REVERT: A 812 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7484 (ptm) REVERT: A 906 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (mt) REVERT: A 978 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7072 (tp40) REVERT: A 988 THR cc_start: 0.7795 (p) cc_final: 0.7463 (m) REVERT: A 1098 LYS cc_start: 0.8236 (mttm) cc_final: 0.7736 (pttt) REVERT: A 1126 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7298 (mtt90) REVERT: B 254 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: B 419 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7711 (mt-10) outliers start: 59 outliers final: 37 residues processed: 246 average time/residue: 1.7245 time to fit residues: 458.1829 Evaluate side-chains 249 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 overall best weight: 7.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 375 ASN A 717 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1095 GLN A1121 GLN B 212 ASN ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13968 Z= 0.323 Angle : 0.602 10.942 18918 Z= 0.313 Chirality : 0.044 0.235 2112 Planarity : 0.005 0.043 2417 Dihedral : 4.809 59.316 1897 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.03 % Allowed : 16.47 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1701 helix: 1.09 (0.18), residues: 801 sheet: -0.62 (0.37), residues: 184 loop : -0.73 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 260 HIS 0.010 0.002 HIS B 59 PHE 0.019 0.002 PHE A 206 TYR 0.021 0.002 TYR A 511 ARG 0.008 0.001 ARG A1073 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 1.502 Fit side-chains REVERT: A 17 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8946 (mttp) REVERT: A 37 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7342 (ptm-80) REVERT: A 319 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 484 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6882 (mpp80) REVERT: A 752 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7037 (tpt-90) REVERT: A 794 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8043 (pp) REVERT: A 906 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8590 (mt) REVERT: A 988 THR cc_start: 0.7681 (p) cc_final: 0.7323 (m) REVERT: A 1098 LYS cc_start: 0.8235 (mttm) cc_final: 0.7801 (pttt) REVERT: A 1126 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7253 (mtt90) REVERT: B 254 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: B 419 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7714 (mt-10) outliers start: 60 outliers final: 41 residues processed: 242 average time/residue: 1.6459 time to fit residues: 427.8196 Evaluate side-chains 247 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 197 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 375 ASN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN A1044 ASN A1095 GLN A1121 GLN B 212 ASN ** B 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13968 Z= 0.328 Angle : 0.617 12.179 18918 Z= 0.320 Chirality : 0.044 0.242 2112 Planarity : 0.004 0.043 2417 Dihedral : 4.820 53.953 1897 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.49 % Allowed : 17.27 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1701 helix: 1.04 (0.18), residues: 801 sheet: -0.64 (0.37), residues: 186 loop : -0.74 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 187 HIS 0.010 0.002 HIS B 59 PHE 0.019 0.002 PHE A 206 TYR 0.020 0.002 TYR A 511 ARG 0.008 0.001 ARG A1073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 1.674 Fit side-chains REVERT: A 17 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8905 (mttp) REVERT: A 37 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7356 (ptm-80) REVERT: A 319 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 484 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6889 (mpp80) REVERT: A 752 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7069 (tpt-90) REVERT: A 794 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 906 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 988 THR cc_start: 0.7677 (p) cc_final: 0.7298 (m) REVERT: A 1010 LYS cc_start: 0.6830 (mmpt) cc_final: 0.6358 (mptt) REVERT: A 1098 LYS cc_start: 0.8239 (mttm) cc_final: 0.7806 (pttt) REVERT: A 1126 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7221 (mtt90) REVERT: B 254 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: B 419 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7713 (mt-10) outliers start: 52 outliers final: 41 residues processed: 234 average time/residue: 1.6757 time to fit residues: 421.2422 Evaluate side-chains 251 residues out of total 1488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 976 LYS Chi-restraints excluded: chain A residue 1042 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 7 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 375 ASN A 717 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN A1044 ASN A1095 GLN A1121 GLN A1140 HIS B 59 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105649 restraints weight = 18214.613| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.59 r_work: 0.3079 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13968 Z= 0.139 Angle : 0.511 12.189 18918 Z= 0.263 Chirality : 0.039 0.167 2112 Planarity : 0.003 0.035 2417 Dihedral : 4.317 53.952 1897 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.96 % Allowed : 17.94 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1701 helix: 1.44 (0.19), residues: 802 sheet: -0.39 (0.38), residues: 172 loop : -0.62 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.004 0.001 HIS A 126 PHE 0.010 0.001 PHE A 206 TYR 0.013 0.001 TYR A1130 ARG 0.008 0.000 ARG A1073 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6773.11 seconds wall clock time: 121 minutes 28.91 seconds (7288.91 seconds total)