Starting phenix.real_space_refine on Thu Mar 21 12:08:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrk_10890/03_2024/6yrk_10890.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15058 atoms to isotropic. 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 19 5.16 5 C 9490 2.51 5 N 2544 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 785": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B GLU 532": "OE1" <-> "OE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 565": "NH1" <-> "NH2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 600": "NH1" <-> "NH2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 700": "OE1" <-> "OE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 717": "OE1" <-> "OE2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 938": "OE1" <-> "OE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B ARG 1038": "NH1" <-> "NH2" Residue "B GLU 1195": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15058 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5982 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 34, 'TRANS': 742} Chain breaks: 3 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9076 Classifications: {'peptide': 1160} Link IDs: {'PTRANS': 71, 'TRANS': 1088} Chain breaks: 5 Time building chain proxies: 7.93, per 1000 atoms: 0.53 Number of scatterers: 15058 At special positions: 0 Unit cell: (121.8, 99.75, 118.65, 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 19 16.00 O 3005 8.00 N 2544 7.00 C 9490 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: 4.65 Conformation dependent library (CDL) restraints added in 2.8 seconds 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 30 sheets defined 22.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.754A pdb=" N VAL A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.620A pdb=" N GLU A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 349 through 360 removed outlier: 3.822A pdb=" N VAL A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.740A pdb=" N VAL A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 596 through 605 removed outlier: 6.402A pdb=" N ALA A 602 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.878A pdb=" N THR A 754 " --> pdb=" O GLN A 751 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 755' Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.866A pdb=" N SER B 102 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.595A pdb=" N LEU B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.052A pdb=" N LEU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 362 through 368 removed outlier: 4.162A pdb=" N MET B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 370 No H-bonds generated for 'chain 'B' and resid 369 through 370' Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.519A pdb=" N THR B 376 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.685A pdb=" N TRP B 408 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.552A pdb=" N LYS B 415 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 567 through 573 removed outlier: 4.261A pdb=" N LEU B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU B 572 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 633 through 641 Processing helix chain 'B' and resid 661 through 670 Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 721 through 727 removed outlier: 4.150A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.533A pdb=" N TYR B 743 " --> pdb=" O TRP B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.784A pdb=" N ASP B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 764 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 863 through 865 No H-bonds generated for 'chain 'B' and resid 863 through 865' Processing helix chain 'B' and resid 896 through 900 Processing helix chain 'B' and resid 903 through 917 removed outlier: 3.502A pdb=" N LEU B 912 " --> pdb=" O ASN B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 939 removed outlier: 3.525A pdb=" N GLU B 938 " --> pdb=" O ASN B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 950 Processing helix chain 'B' and resid 961 through 969 Processing helix chain 'B' and resid 1051 through 1056 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1081 through 1084 Processing helix chain 'B' and resid 1119 through 1123 removed outlier: 3.758A pdb=" N ASN B1122 " --> pdb=" O ASN B1119 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS B1123 " --> pdb=" O THR B1120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1119 through 1123' Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.809A pdb=" N LEU B1143 " --> pdb=" O SER B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1153 removed outlier: 3.592A pdb=" N ILE B1149 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B1152 " --> pdb=" O ASN B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1203 Processing helix chain 'B' and resid 1207 through 1211 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 72 removed outlier: 5.683A pdb=" N ILE A 66 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 81 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 68 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A 109 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN A 131 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 111 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS A 129 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 113 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ASN A 335 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 131 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.221A pdb=" N GLY A 406 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.589A pdb=" N ASN A 344 " --> pdb=" O TRP A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 391 removed outlier: 4.907A pdb=" N ILE A 385 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 400 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 387 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 398 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE A 541 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AB2, first strand: chain 'A' and resid 585 through 586 removed outlier: 4.769A pdb=" N LYS A 611 " --> pdb=" O GLU A 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 626 through 633 removed outlier: 4.367A pdb=" N LEU A 629 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 649 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 631 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 647 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR A 646 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 661 " --> pdb=" O TYR A 646 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 626 through 633 removed outlier: 4.367A pdb=" N LEU A 629 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 649 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 631 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 647 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR A 646 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 661 " --> pdb=" O TYR A 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 704 removed outlier: 6.859A pdb=" N ILE A 713 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 701 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 703 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 709 " --> pdb=" O TYR A 703 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE A 735 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 769 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL A 737 " --> pdb=" O SER A 767 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 775 through 780 removed outlier: 6.907A pdb=" N ILE A 790 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 779 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 788 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 801 " --> pdb=" O ASP A 812 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.955A pdb=" N ARG B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AC1, first strand: chain 'B' and resid 187 through 193 removed outlier: 6.539A pdb=" N LEU B 204 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 191 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN B 193 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 200 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA B 338 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N HIS B 360 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 340 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 358 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER B 342 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC5, first strand: chain 'B' and resid 457 through 460 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 545 removed outlier: 4.761A pdb=" N VAL B 539 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR B 554 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 541 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 549 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 695 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B 750 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 697 " --> pdb=" O GLN B 748 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AC8, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AC9, first strand: chain 'B' and resid 921 through 923 Processing sheet with id=AD1, first strand: chain 'B' and resid 1013 through 1014 removed outlier: 3.824A pdb=" N PHE B1020 " --> pdb=" O PHE B1031 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY B1214 " --> pdb=" O ILE B1044 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B1046 " --> pdb=" O GLY B1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 5.071A pdb=" N LEU B1078 " --> pdb=" O LYS B1065 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1067 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B1076 " --> pdb=" O SER B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1228 through 1230 399 hydrogen bonds defined for protein. 996 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: 6.07 Time building geometry restraints manager: 5.18 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: 3183 1.33 - 1.45: 3878 1.45 - 1.58: 8294 1.58 - 1.70: 19 1.70 - 1.82: 34 Bond restraints: 15408 Sorted by residual: bond pdb=" SD MET B 537 " pdb=" CE MET B 537 " ideal model delta sigma weight residual 1.791 1.634 0.157 2.50e-02 1.60e+03 3.93e+01 bond pdb=" SD MET B 557 " pdb=" CE MET B 557 " ideal model delta sigma weight residual 1.791 1.642 0.149 2.50e-02 1.60e+03 3.56e+01 bond pdb=" CA PHE B1020 " pdb=" C PHE B1020 " ideal model delta sigma weight residual 1.522 1.594 -0.072 1.24e-02 6.50e+03 3.37e+01 bond pdb=" SD MET B 457 " pdb=" CE MET B 457 " ideal model delta sigma weight residual 1.791 1.658 0.133 2.50e-02 1.60e+03 2.81e+01 bond pdb=" CA ILE A 502 " pdb=" C ILE A 502 " ideal model delta sigma weight residual 1.522 1.587 -0.065 1.24e-02 6.50e+03 2.74e+01 ... (remaining 15403 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.28: 387 105.28 - 112.75: 6711 112.75 - 120.22: 7505 120.22 - 127.69: 6063 127.69 - 135.17: 288 Bond angle restraints: 20954 Sorted by residual: angle pdb=" CA ASN B 99 " pdb=" CB ASN B 99 " pdb=" CG ASN B 99 " ideal model delta sigma weight residual 112.60 121.90 -9.30 1.00e+00 1.00e+00 8.64e+01 angle pdb=" CA ASP B 701 " pdb=" CB ASP B 701 " pdb=" CG ASP B 701 " ideal model delta sigma weight residual 112.60 121.13 -8.53 1.00e+00 1.00e+00 7.27e+01 angle pdb=" C ALA B 987 " pdb=" N ASP B 988 " pdb=" CA ASP B 988 " ideal model delta sigma weight residual 121.02 133.40 -12.38 1.48e+00 4.57e-01 7.00e+01 angle pdb=" C GLN B 849 " pdb=" N VAL B 850 " pdb=" CA VAL B 850 " ideal model delta sigma weight residual 120.77 131.47 -10.70 1.46e+00 4.69e-01 5.37e+01 angle pdb=" N GLN B 849 " pdb=" CA GLN B 849 " pdb=" C GLN B 849 " ideal model delta sigma weight residual 111.56 101.53 10.03 1.38e+00 5.25e-01 5.28e+01 ... (remaining 20949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7902 17.86 - 35.72: 807 35.72 - 53.58: 305 53.58 - 71.45: 108 71.45 - 89.31: 40 Dihedral angle restraints: 9162 sinusoidal: 3583 harmonic: 5579 Sorted by residual: dihedral pdb=" C ASP A 723 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " pdb=" CB ASP A 723 " ideal model delta harmonic sigma weight residual -122.60 -112.13 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" N ASN B 150 " pdb=" C ASN B 150 " pdb=" CA ASN B 150 " pdb=" CB ASN B 150 " ideal model delta harmonic sigma weight residual 122.80 133.22 -10.42 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C GLN A 104 " pdb=" N GLN A 104 " pdb=" CA GLN A 104 " pdb=" CB GLN A 104 " ideal model delta harmonic sigma weight residual -122.60 -132.58 9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 9159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1010 0.078 - 0.156: 832 0.156 - 0.234: 392 0.234 - 0.312: 78 0.312 - 0.390: 6 Chirality restraints: 2318 Sorted by residual: chirality pdb=" CA ALA B 538 " pdb=" N ALA B 538 " pdb=" C ALA B 538 " pdb=" CB ALA B 538 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASN B 150 " pdb=" N ASN B 150 " pdb=" C ASN B 150 " pdb=" CB ASN B 150 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA LYS A 156 " pdb=" N LYS A 156 " pdb=" C LYS A 156 " pdb=" CB LYS A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2315 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 658 " -0.066 2.00e-02 2.50e+03 3.47e-02 2.41e+01 pdb=" CG TYR B 658 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 658 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 658 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 658 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 658 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 658 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 658 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 669 " -0.010 2.00e-02 2.50e+03 2.54e-02 1.61e+01 pdb=" CG TRP B 669 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 669 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 669 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 669 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TRP B 669 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 669 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 669 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 669 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP B 669 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 408 " -0.048 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP B 408 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 408 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 408 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP B 408 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 408 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 408 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 408 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 408 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 408 " -0.032 2.00e-02 2.50e+03 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6258 2.96 - 3.44: 14739 3.44 - 3.93: 27510 3.93 - 4.41: 31715 4.41 - 4.90: 51435 Nonbonded interactions: 131657 Sorted by model distance: nonbonded pdb=" N SER B 856 " pdb=" N THR B 857 " model vdw 2.473 2.560 nonbonded pdb=" N GLN B 849 " pdb=" N VAL B 850 " model vdw 2.474 2.560 nonbonded pdb=" ND2 ASN A 806 " pdb=" O ASP B 701 " model vdw 2.481 2.520 nonbonded pdb=" N THR A 687 " pdb=" O THR A 687 " model vdw 2.500 2.496 nonbonded pdb=" O GLN A 796 " pdb=" NE2 GLN A 796 " model vdw 2.503 2.520 ... (remaining 131652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 41.490 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4598 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 : 0.014 0.157 15408 Z= 0.883 Angle : 1.850 13.366 20954 Z= 1.238 Chirality : 0.119 0.390 2318 Planarity : 0.008 0.038 2742 Dihedral : 18.902 89.307 5572 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.36 % Favored : 93.17 % Rotamer: Outliers : 12.77 % Allowed : 10.93 % Favored : 76.30 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 1917 helix: -2.78 (0.22), residues: 293 sheet: -0.90 (0.27), residues: 301 loop : -1.64 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.011 TRP B1056 HIS 0.015 0.004 HIS B 381 PHE 0.043 0.008 PHE A 397 TYR 0.066 0.010 TYR B 658 ARG 0.013 0.002 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 314 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.5026 (OUTLIER) cc_final: 0.4523 (t70) REVERT: A 136 ASN cc_start: 0.1348 (OUTLIER) cc_final: -0.1530 (t0) REVERT: A 189 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5204 (m-40) REVERT: A 254 SER cc_start: 0.2811 (OUTLIER) cc_final: 0.2578 (t) REVERT: A 366 THR cc_start: 0.4866 (OUTLIER) cc_final: 0.4640 (p) REVERT: A 670 SER cc_start: 0.2743 (OUTLIER) cc_final: 0.2282 (p) REVERT: B 448 GLU cc_start: 0.2298 (OUTLIER) cc_final: 0.0978 (mt-10) REVERT: B 683 VAL cc_start: 0.6851 (t) cc_final: 0.6590 (p) REVERT: B 728 GLN cc_start: 0.4684 (OUTLIER) cc_final: 0.4467 (mt0) REVERT: B 1136 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6695 (m-40) outliers start: 216 outliers final: 35 residues processed: 491 average time/residue: 0.2913 time to fit residues: 204.0202 Evaluate side-chains 196 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 475 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 662 ASN A 722 HIS A 748 ASN B 59 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN B 196 HIS B 360 HIS B 382 HIS B 395 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 ASN B 684 ASN B 735 ASN B 745 ASN B 967 HIS B1011 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 GLN B1119 ASN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4887 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15408 Z= 0.217 Angle : 0.688 8.926 20954 Z= 0.368 Chirality : 0.047 0.244 2318 Planarity : 0.005 0.078 2742 Dihedral : 5.368 33.526 2032 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 1917 helix: -0.88 (0.28), residues: 300 sheet: -0.06 (0.27), residues: 341 loop : -0.94 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 220 HIS 0.009 0.001 HIS A 722 PHE 0.030 0.002 PHE B 761 TYR 0.032 0.002 TYR B 201 ARG 0.013 0.001 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.5832 (mt) cc_final: 0.4870 (mt) REVERT: B 148 MET cc_start: -0.1413 (mmt) cc_final: -0.1833 (mmt) REVERT: B 923 ILE cc_start: 0.5314 (mm) cc_final: 0.5020 (mm) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2816 time to fit residues: 80.7950 Evaluate side-chains 119 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 503 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 HIS ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 ASN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5217 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15408 Z= 0.270 Angle : 0.658 9.533 20954 Z= 0.348 Chirality : 0.045 0.194 2318 Planarity : 0.004 0.046 2742 Dihedral : 5.332 32.847 2032 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 1917 helix: -0.59 (0.28), residues: 305 sheet: 0.08 (0.27), residues: 339 loop : -0.92 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1004 HIS 0.006 0.001 HIS A 371 PHE 0.034 0.002 PHE A 373 TYR 0.020 0.002 TYR B 201 ARG 0.009 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 PHE cc_start: 0.5692 (m-80) cc_final: 0.5278 (m-10) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.3003 time to fit residues: 73.1126 Evaluate side-chains 106 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 344 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 302 HIS ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 HIS ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5296 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15408 Z= 0.235 Angle : 0.615 9.191 20954 Z= 0.322 Chirality : 0.044 0.169 2318 Planarity : 0.005 0.104 2742 Dihedral : 5.229 31.331 2032 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 1917 helix: -0.33 (0.30), residues: 285 sheet: 0.15 (0.28), residues: 339 loop : -0.76 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 220 HIS 0.004 0.001 HIS A 371 PHE 0.020 0.002 PHE B 761 TYR 0.015 0.002 TYR B 880 ARG 0.007 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: -0.0339 (mmt) cc_final: -0.0674 (mmt) REVERT: B 703 LEU cc_start: 0.7517 (mm) cc_final: 0.7270 (mt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2941 time to fit residues: 64.7057 Evaluate side-chains 98 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15408 Z= 0.192 Angle : 0.574 7.487 20954 Z= 0.302 Chirality : 0.043 0.185 2318 Planarity : 0.004 0.083 2742 Dihedral : 5.047 29.561 2032 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 1917 helix: -0.24 (0.31), residues: 285 sheet: 0.08 (0.27), residues: 339 loop : -0.70 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 347 HIS 0.003 0.001 HIS A 371 PHE 0.018 0.002 PHE A 809 TYR 0.026 0.001 TYR B1041 ARG 0.014 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1211 ILE cc_start: 0.6225 (mp) cc_final: 0.5943 (tp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2790 time to fit residues: 58.0700 Evaluate side-chains 104 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 186 optimal weight: 0.0000 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 183 GLN A 211 ASN A 380 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN B 116 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5233 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15408 Z= 0.158 Angle : 0.568 10.743 20954 Z= 0.295 Chirality : 0.043 0.166 2318 Planarity : 0.004 0.096 2742 Dihedral : 4.915 29.687 2032 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1917 helix: -0.28 (0.31), residues: 294 sheet: 0.15 (0.28), residues: 328 loop : -0.70 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 503 HIS 0.004 0.001 HIS B 574 PHE 0.030 0.002 PHE B 761 TYR 0.022 0.001 TYR B 662 ARG 0.008 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: -0.0215 (mmt) cc_final: -0.0528 (mmt) REVERT: B 1211 ILE cc_start: 0.6140 (mp) cc_final: 0.5890 (tp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2830 time to fit residues: 58.6212 Evaluate side-chains 99 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 0.4980 chunk 157 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 531 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 660 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15408 Z= 0.179 Angle : 0.572 8.609 20954 Z= 0.296 Chirality : 0.043 0.173 2318 Planarity : 0.005 0.164 2742 Dihedral : 4.918 28.575 2032 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.06 % Allowed : 1.12 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 1917 helix: -0.41 (0.31), residues: 289 sheet: 0.22 (0.28), residues: 318 loop : -0.72 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 220 HIS 0.006 0.001 HIS B 574 PHE 0.026 0.002 PHE B 761 TYR 0.018 0.001 TYR B1121 ARG 0.013 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.0084 (mmt) cc_final: -0.0210 (mmt) REVERT: B 799 ILE cc_start: 0.7791 (mp) cc_final: 0.7409 (mm) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2593 time to fit residues: 52.8959 Evaluate side-chains 101 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 HIS ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15408 Z= 0.167 Angle : 0.562 9.031 20954 Z= 0.295 Chirality : 0.043 0.173 2318 Planarity : 0.005 0.144 2742 Dihedral : 4.919 28.213 2032 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1917 helix: -0.37 (0.31), residues: 292 sheet: 0.30 (0.28), residues: 322 loop : -0.72 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 374 HIS 0.010 0.001 HIS B 810 PHE 0.026 0.002 PHE B 170 TYR 0.018 0.001 TYR B1121 ARG 0.010 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.7700 (p0) cc_final: 0.7475 (p0) REVERT: B 148 MET cc_start: 0.0026 (mmt) cc_final: -0.0213 (mmt) REVERT: B 799 ILE cc_start: 0.7544 (mp) cc_final: 0.7294 (mm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2487 time to fit residues: 50.1656 Evaluate side-chains 102 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 163 optimal weight: 0.0980 chunk 172 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN B 924 ASN B 962 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15408 Z= 0.179 Angle : 0.568 9.255 20954 Z= 0.294 Chirality : 0.043 0.204 2318 Planarity : 0.005 0.120 2742 Dihedral : 4.894 27.724 2032 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1917 helix: -0.45 (0.31), residues: 298 sheet: 0.20 (0.28), residues: 325 loop : -0.72 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 220 HIS 0.004 0.001 HIS A 371 PHE 0.031 0.002 PHE B 761 TYR 0.021 0.002 TYR B 450 ARG 0.007 0.000 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.0249 (mmt) cc_final: 0.0047 (mmt) REVERT: B 588 ASP cc_start: 0.6784 (p0) cc_final: 0.6427 (p0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2713 time to fit residues: 55.6596 Evaluate side-chains 104 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 153 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS B 453 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.8117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15408 Z= 0.387 Angle : 0.780 13.499 20954 Z= 0.408 Chirality : 0.048 0.204 2318 Planarity : 0.006 0.129 2742 Dihedral : 5.914 30.736 2032 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.15 % Favored : 92.80 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 1917 helix: -1.35 (0.28), residues: 307 sheet: -0.28 (0.28), residues: 330 loop : -1.11 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 740 HIS 0.012 0.002 HIS A 371 PHE 0.044 0.003 PHE B 170 TYR 0.026 0.003 TYR B1041 ARG 0.014 0.001 ARG B 536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8100 (tmm) cc_final: 0.7562 (tmm) REVERT: B 588 ASP cc_start: 0.7025 (p0) cc_final: 0.6751 (p0) REVERT: B 610 GLN cc_start: 0.2717 (OUTLIER) cc_final: 0.2323 (pp30) REVERT: B 910 LEU cc_start: 0.8085 (mt) cc_final: 0.7754 (mt) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2474 time to fit residues: 50.5413 Evaluate side-chains 98 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 360 HIS B 430 HIS ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN ** B1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.074691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.064424 restraints weight = 104896.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.065824 restraints weight = 72351.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.066828 restraints weight = 54514.582| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15408 Z= 0.189 Angle : 0.602 11.152 20954 Z= 0.313 Chirality : 0.044 0.175 2318 Planarity : 0.005 0.108 2742 Dihedral : 5.348 28.396 2032 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 1917 helix: -0.76 (0.30), residues: 291 sheet: -0.11 (0.29), residues: 313 loop : -0.89 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 220 HIS 0.005 0.001 HIS B 382 PHE 0.037 0.002 PHE B 761 TYR 0.023 0.001 TYR B1121 ARG 0.008 0.001 ARG B 817 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.98 seconds wall clock time: 51 minutes 50.37 seconds (3110.37 seconds total)