Starting phenix.real_space_refine on Wed Mar 4 21:04:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sti_25429/03_2026/7sti_25429.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 3406 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 110 5.16 5 C 8587 2.51 5 N 2326 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6585 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 770} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6570 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 769} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 3.05, per 1000 atoms: 0.23 Number of scatterers: 13531 At special positions: 0 Unit cell: (122.04, 105.84, 180.36, 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 110 16.00 O 2508 8.00 N 2326 7.00 C 8587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 682 " - pdb=" SG CYS B 685 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.02 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 427.6 milliseconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 34 sheets defined 13.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.559A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.608A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.638A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.720A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 688 through 714 removed outlier: 3.796A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'B' and resid 17 through 24 removed outlier: 4.017A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.645A pdb=" N ASP B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 324 through 329 removed outlier: 4.299A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.905A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.169A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 688 through 712 removed outlier: 3.851A pdb=" N LEU B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 709 " --> pdb=" O PHE B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 869 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.089A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.733A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.842A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.842A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 94 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 63 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 96 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 8.546A pdb=" N LYS A 310 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE A 336 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS A 312 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 319 removed outlier: 6.282A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.347A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.752A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.274A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.989A pdb=" N GLY A 778 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 819 through 822 Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 862 removed outlier: 3.554A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 880 through 881 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.556A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 145 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 119 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 147 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.066A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.807A pdb=" N SER B 339 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.807A pdb=" N SER B 339 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.652A pdb=" N THR B 560 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 590 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 598 through 605 removed outlier: 6.741A pdb=" N LYS B 614 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 603 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 612 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.501A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.501A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 803 " --> pdb=" O TYR B 779 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 818 through 822 Processing sheet with id=AD7, first strand: chain 'B' and resid 856 through 862 removed outlier: 3.613A pdb=" N SER B 883 " --> pdb=" O ARG B 850 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 825 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: 2.43 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4432 1.34 - 1.46: 3280 1.46 - 1.58: 6013 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13859 Sorted by residual: bond pdb=" C TRP B 615 " pdb=" N LYS B 616 " ideal model delta sigma weight residual 1.327 1.275 0.052 1.71e-02 3.42e+03 9.10e+00 bond pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" C LEU B 360 " pdb=" N ILE B 361 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.21e+00 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.20e-02 6.94e+03 1.73e+00 bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.29e-02 6.01e+03 1.50e+00 ... (remaining 13854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 18400 2.01 - 4.03: 345 4.03 - 6.04: 24 6.04 - 8.06: 9 8.06 - 10.07: 1 Bond angle restraints: 18779 Sorted by residual: angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 111.24 104.00 7.24 1.38e+00 5.25e-01 2.76e+01 angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 112.41 105.74 6.67 1.30e+00 5.92e-01 2.63e+01 angle pdb=" N GLY B 347 " pdb=" CA GLY B 347 " pdb=" C GLY B 347 " ideal model delta sigma weight residual 114.92 108.82 6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" C PRO A 307 " pdb=" N CYS A 308 " pdb=" CA CYS A 308 " ideal model delta sigma weight residual 121.80 131.87 -10.07 2.44e+00 1.68e-01 1.70e+01 angle pdb=" N GLY B 650 " pdb=" CA GLY B 650 " pdb=" C GLY B 650 " ideal model delta sigma weight residual 115.67 109.90 5.77 1.59e+00 3.96e-01 1.31e+01 ... (remaining 18774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7530 17.10 - 34.20: 712 34.20 - 51.30: 131 51.30 - 68.39: 25 68.39 - 85.49: 15 Dihedral angle restraints: 8413 sinusoidal: 3513 harmonic: 4900 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 176.70 -83.70 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 62 " pdb=" CB CYS C 62 " ideal model delta sinusoidal sigma weight residual 93.00 14.93 78.07 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -151.89 65.89 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 8410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1448 0.041 - 0.081: 413 0.081 - 0.122: 158 0.122 - 0.162: 16 0.162 - 0.203: 2 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU B 350 " pdb=" CB LEU B 350 " pdb=" CD1 LEU B 350 " pdb=" CD2 LEU B 350 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2034 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 308 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 309 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 455 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASN B 455 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 455 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 456 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 829 " 0.021 2.00e-02 2.50e+03 1.73e-02 4.47e+00 pdb=" CG HIS B 829 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS B 829 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 829 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 829 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 829 " 0.014 2.00e-02 2.50e+03 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 12156 3.16 - 3.74: 23419 3.74 - 4.32: 32215 4.32 - 4.90: 49919 Nonbonded interactions: 117941 Sorted by model distance: nonbonded pdb=" OE2 GLU A 698 " pdb=" OH TYR B 144 " model vdw 2.001 3.040 nonbonded pdb=" O LYS B 557 " pdb=" OG1 THR B 560 " model vdw 2.094 3.040 nonbonded pdb=" OD1 ASP B 812 " pdb=" OG SER B 890 " model vdw 2.105 3.040 nonbonded pdb=" O LYS B 557 " pdb=" OG1 THR B 590 " model vdw 2.111 3.040 nonbonded pdb=" OG SER B 50 " pdb=" O ASP B 74 " model vdw 2.130 3.040 ... (remaining 117936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 518 or resid 528 through 712 or resid 756 throug \ h 905)) selection = (chain 'B' and (resid 3 through 314 or resid 317 through 346 or resid 351 throug \ h 539 or resid 547 through 905)) } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13895 Z= 0.180 Angle : 0.670 10.074 18851 Z= 0.373 Chirality : 0.043 0.203 2037 Planarity : 0.004 0.080 2427 Dihedral : 13.500 85.493 5137 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.80 % Favored : 92.02 % Rotamer: Outliers : 0.20 % Allowed : 0.26 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1642 helix: -1.06 (0.39), residues: 168 sheet: -0.27 (0.29), residues: 355 loop : -1.12 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 118 TYR 0.016 0.001 TYR A 579 PHE 0.019 0.002 PHE A 701 TRP 0.019 0.002 TRP B 412 HIS 0.012 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00362 (13859) covalent geometry : angle 0.66866 (18779) SS BOND : bond 0.00264 ( 36) SS BOND : angle 1.00567 ( 72) hydrogen bonds : bond 0.30058 ( 313) hydrogen bonds : angle 10.02451 ( 825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 MET cc_start: 0.9232 (mpp) cc_final: 0.9002 (mpp) REVERT: A 553 MET cc_start: 0.9380 (tpt) cc_final: 0.9093 (tpp) REVERT: B 72 LEU cc_start: 0.9616 (tp) cc_final: 0.9347 (tp) REVERT: B 410 GLN cc_start: 0.9103 (pt0) cc_final: 0.8815 (mp10) REVERT: B 852 TYR cc_start: 0.9623 (t80) cc_final: 0.9397 (p90) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.1074 time to fit residues: 10.5366 Evaluate side-chains 48 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN C 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.024310 restraints weight = 222519.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.025131 restraints weight = 132425.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.025674 restraints weight = 92242.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.026097 restraints weight = 72447.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.026406 restraints weight = 60043.609| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13895 Z= 0.197 Angle : 0.649 9.382 18851 Z= 0.342 Chirality : 0.045 0.177 2037 Planarity : 0.005 0.082 2427 Dihedral : 4.926 26.697 1828 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.72 % Rotamer: Outliers : 0.20 % Allowed : 6.22 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.21), residues: 1642 helix: -0.97 (0.38), residues: 179 sheet: -0.20 (0.29), residues: 345 loop : -1.14 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 576 TYR 0.018 0.002 TYR A 562 PHE 0.033 0.002 PHE B 701 TRP 0.015 0.002 TRP B 551 HIS 0.011 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00418 (13859) covalent geometry : angle 0.64703 (18779) SS BOND : bond 0.00309 ( 36) SS BOND : angle 1.00846 ( 72) hydrogen bonds : bond 0.05609 ( 313) hydrogen bonds : angle 7.91401 ( 825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9551 (tp) cc_final: 0.9301 (tp) REVERT: B 76 PHE cc_start: 0.9505 (m-10) cc_final: 0.9230 (m-10) REVERT: B 110 MET cc_start: 0.9042 (mmm) cc_final: 0.8812 (mmm) REVERT: B 852 TYR cc_start: 0.9380 (t80) cc_final: 0.9052 (p90) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.0996 time to fit residues: 8.6286 Evaluate side-chains 46 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 11 optimal weight: 9.9990 chunk 114 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 165 optimal weight: 0.0050 chunk 23 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.036425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.024239 restraints weight = 231939.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.025056 restraints weight = 136006.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.025602 restraints weight = 94711.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026020 restraints weight = 73885.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.026276 restraints weight = 61475.680| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13895 Z= 0.197 Angle : 0.638 9.288 18851 Z= 0.335 Chirality : 0.045 0.192 2037 Planarity : 0.004 0.082 2427 Dihedral : 4.969 26.396 1828 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.16 % Favored : 91.66 % Rotamer: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1642 helix: -1.02 (0.38), residues: 178 sheet: -0.42 (0.28), residues: 355 loop : -1.16 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 851 TYR 0.012 0.002 TYR A 562 PHE 0.028 0.002 PHE B 701 TRP 0.019 0.002 TRP B 412 HIS 0.011 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00417 (13859) covalent geometry : angle 0.63653 (18779) SS BOND : bond 0.00274 ( 36) SS BOND : angle 0.95394 ( 72) hydrogen bonds : bond 0.05237 ( 313) hydrogen bonds : angle 7.70951 ( 825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9587 (tp) cc_final: 0.9365 (tp) REVERT: B 76 PHE cc_start: 0.9618 (m-10) cc_final: 0.9378 (m-10) REVERT: B 806 MET cc_start: 0.8838 (mpp) cc_final: 0.8492 (mpp) REVERT: B 852 TYR cc_start: 0.9415 (t80) cc_final: 0.9058 (p90) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.0958 time to fit residues: 7.8123 Evaluate side-chains 45 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 126 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 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 343 ASN A 521 GLN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.035584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023479 restraints weight = 234259.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.024272 restraints weight = 141804.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.024758 restraints weight = 98708.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.025154 restraints weight = 78630.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.025456 restraints weight = 65376.134| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 13895 Z= 0.249 Angle : 0.686 9.233 18851 Z= 0.356 Chirality : 0.045 0.208 2037 Planarity : 0.005 0.083 2427 Dihedral : 5.180 26.228 1828 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 26.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.83 % Favored : 90.99 % Rotamer: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1642 helix: -1.07 (0.38), residues: 181 sheet: -0.74 (0.27), residues: 369 loop : -1.23 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 409 TYR 0.032 0.002 TYR A 277 PHE 0.028 0.002 PHE B 701 TRP 0.020 0.002 TRP B 412 HIS 0.012 0.002 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00528 (13859) covalent geometry : angle 0.68411 (18779) SS BOND : bond 0.00331 ( 36) SS BOND : angle 1.08419 ( 72) hydrogen bonds : bond 0.04786 ( 313) hydrogen bonds : angle 7.71184 ( 825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.8974 (mmp) cc_final: 0.8501 (mmm) REVERT: B 110 MET cc_start: 0.9140 (mmm) cc_final: 0.8819 (mmm) REVERT: B 553 MET cc_start: 0.9213 (mpp) cc_final: 0.9005 (mpp) REVERT: B 852 TYR cc_start: 0.9470 (t80) cc_final: 0.9073 (p90) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.1064 time to fit residues: 8.6119 Evaluate side-chains 43 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 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 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.036058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023786 restraints weight = 230326.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.024583 restraints weight = 139058.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.025084 restraints weight = 97125.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.025530 restraints weight = 75661.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.025799 restraints weight = 63057.451| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13895 Z= 0.162 Angle : 0.602 9.250 18851 Z= 0.316 Chirality : 0.045 0.179 2037 Planarity : 0.004 0.084 2427 Dihedral : 5.027 25.647 1828 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.28 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1642 helix: -0.86 (0.39), residues: 175 sheet: -0.65 (0.28), residues: 354 loop : -1.15 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 863 TYR 0.016 0.001 TYR B 144 PHE 0.030 0.002 PHE B 701 TRP 0.019 0.002 TRP B 412 HIS 0.010 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00354 (13859) covalent geometry : angle 0.60007 (18779) SS BOND : bond 0.00270 ( 36) SS BOND : angle 0.99307 ( 72) hydrogen bonds : bond 0.04362 ( 313) hydrogen bonds : angle 7.34421 ( 825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9486 (mp) cc_final: 0.9206 (pt) REVERT: B 38 MET cc_start: 0.8964 (mmp) cc_final: 0.8484 (mmm) REVERT: B 110 MET cc_start: 0.9111 (mmm) cc_final: 0.8769 (mmm) REVERT: B 806 MET cc_start: 0.8831 (mpp) cc_final: 0.8452 (mpp) REVERT: B 852 TYR cc_start: 0.9439 (t80) cc_final: 0.9026 (p90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0918 time to fit residues: 7.3373 Evaluate side-chains 45 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN A 275 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.036737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.024414 restraints weight = 226395.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.025260 restraints weight = 133713.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.025812 restraints weight = 93107.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.026241 restraints weight = 73104.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.026567 restraints weight = 60448.135| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13895 Z= 0.112 Angle : 0.583 9.367 18851 Z= 0.302 Chirality : 0.046 0.181 2037 Planarity : 0.004 0.084 2427 Dihedral : 4.800 25.564 1828 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1642 helix: -0.74 (0.39), residues: 173 sheet: -0.39 (0.29), residues: 343 loop : -1.05 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 47 TYR 0.012 0.001 TYR B 882 PHE 0.031 0.001 PHE B 701 TRP 0.014 0.001 TRP B 412 HIS 0.007 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00254 (13859) covalent geometry : angle 0.58218 (18779) SS BOND : bond 0.00203 ( 36) SS BOND : angle 0.85211 ( 72) hydrogen bonds : bond 0.03904 ( 313) hydrogen bonds : angle 6.86082 ( 825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9483 (mp) cc_final: 0.9195 (pt) REVERT: A 831 MET cc_start: 0.9380 (tpt) cc_final: 0.9179 (tpt) REVERT: B 38 MET cc_start: 0.8896 (mmp) cc_final: 0.8307 (mmm) REVERT: B 76 PHE cc_start: 0.9599 (m-10) cc_final: 0.9377 (m-10) REVERT: B 553 MET cc_start: 0.9176 (mpp) cc_final: 0.8970 (mpp) REVERT: B 806 MET cc_start: 0.8819 (mpp) cc_final: 0.8509 (mpp) REVERT: B 852 TYR cc_start: 0.9449 (t80) cc_final: 0.9018 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1014 time to fit residues: 8.8103 Evaluate side-chains 46 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.023209 restraints weight = 242870.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.023977 restraints weight = 145471.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.024520 restraints weight = 101981.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.024895 restraints weight = 79920.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.025153 restraints weight = 66642.205| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 13895 Z= 0.273 Angle : 0.708 9.004 18851 Z= 0.368 Chirality : 0.046 0.188 2037 Planarity : 0.005 0.087 2427 Dihedral : 5.256 25.320 1828 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.38 % Favored : 90.50 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.21), residues: 1642 helix: -0.93 (0.39), residues: 173 sheet: -0.64 (0.29), residues: 347 loop : -1.19 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 863 TYR 0.018 0.002 TYR A 562 PHE 0.027 0.002 PHE B 701 TRP 0.016 0.002 TRP B 412 HIS 0.010 0.002 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00577 (13859) covalent geometry : angle 0.70564 (18779) SS BOND : bond 0.00344 ( 36) SS BOND : angle 1.14971 ( 72) hydrogen bonds : bond 0.04647 ( 313) hydrogen bonds : angle 7.57047 ( 825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9417 (mp) cc_final: 0.9063 (pt) REVERT: A 831 MET cc_start: 0.9402 (tpt) cc_final: 0.9116 (tpt) REVERT: B 38 MET cc_start: 0.9108 (mmp) cc_final: 0.8614 (mmm) REVERT: B 553 MET cc_start: 0.9071 (mpp) cc_final: 0.8808 (mpp) REVERT: B 852 TYR cc_start: 0.9475 (t80) cc_final: 0.9036 (p90) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0955 time to fit residues: 7.6909 Evaluate side-chains 43 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 138 optimal weight: 0.0170 chunk 157 optimal weight: 9.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.035943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.023936 restraints weight = 234946.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.024756 restraints weight = 139401.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.025274 restraints weight = 97486.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025688 restraints weight = 76438.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.025964 restraints weight = 63504.999| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13895 Z= 0.138 Angle : 0.601 9.211 18851 Z= 0.312 Chirality : 0.045 0.190 2037 Planarity : 0.004 0.089 2427 Dihedral : 5.005 25.137 1828 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.16 % Favored : 91.72 % Rotamer: Outliers : 0.07 % Allowed : 0.98 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.21), residues: 1642 helix: -0.79 (0.38), residues: 179 sheet: -0.64 (0.28), residues: 356 loop : -1.11 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 863 TYR 0.011 0.001 TYR A 507 PHE 0.030 0.001 PHE B 701 TRP 0.015 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00306 (13859) covalent geometry : angle 0.59982 (18779) SS BOND : bond 0.00228 ( 36) SS BOND : angle 0.86953 ( 72) hydrogen bonds : bond 0.03961 ( 313) hydrogen bonds : angle 7.07494 ( 825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9546 (mp) cc_final: 0.9236 (pt) REVERT: A 831 MET cc_start: 0.9401 (tpt) cc_final: 0.9109 (tpt) REVERT: B 38 MET cc_start: 0.9161 (mmp) cc_final: 0.8556 (mmm) REVERT: B 553 MET cc_start: 0.9118 (mpp) cc_final: 0.8917 (mpp) REVERT: B 806 MET cc_start: 0.8926 (mpp) cc_final: 0.8490 (mpp) REVERT: B 852 TYR cc_start: 0.9448 (t80) cc_final: 0.8971 (p90) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.0913 time to fit residues: 7.4310 Evaluate side-chains 44 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 455 ASN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.034575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.022750 restraints weight = 249607.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.023492 restraints weight = 148901.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.024017 restraints weight = 104450.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.024358 restraints weight = 81470.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.024606 restraints weight = 68512.543| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 13895 Z= 0.339 Angle : 0.816 9.390 18851 Z= 0.420 Chirality : 0.048 0.255 2037 Planarity : 0.006 0.090 2427 Dihedral : 5.752 25.449 1828 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 34.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.87 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.21), residues: 1642 helix: -1.21 (0.38), residues: 167 sheet: -0.83 (0.29), residues: 344 loop : -1.36 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 454 TYR 0.022 0.002 TYR A 562 PHE 0.027 0.003 PHE B 76 TRP 0.020 0.003 TRP B 559 HIS 0.015 0.002 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00716 (13859) covalent geometry : angle 0.81319 (18779) SS BOND : bond 0.00439 ( 36) SS BOND : angle 1.33559 ( 72) hydrogen bonds : bond 0.04996 ( 313) hydrogen bonds : angle 8.01042 ( 825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9296 (mp) cc_final: 0.8888 (pt) REVERT: B 38 MET cc_start: 0.9205 (mmp) cc_final: 0.8809 (mmm) REVERT: B 112 ILE cc_start: 0.9622 (mt) cc_final: 0.9404 (mm) REVERT: B 553 MET cc_start: 0.9081 (mpp) cc_final: 0.8797 (mpp) REVERT: B 806 MET cc_start: 0.8944 (mpp) cc_final: 0.8586 (mpp) REVERT: B 852 TYR cc_start: 0.9528 (t80) cc_final: 0.9080 (p90) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0747 time to fit residues: 6.1167 Evaluate side-chains 41 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.035729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023686 restraints weight = 231871.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.024464 restraints weight = 138236.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.024981 restraints weight = 96757.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.025394 restraints weight = 76171.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.025716 restraints weight = 62940.819| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13895 Z= 0.150 Angle : 0.627 9.184 18851 Z= 0.326 Chirality : 0.046 0.201 2037 Planarity : 0.004 0.092 2427 Dihedral : 5.263 25.109 1828 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.16 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.21), residues: 1642 helix: -0.85 (0.38), residues: 176 sheet: -0.62 (0.29), residues: 327 loop : -1.23 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 863 TYR 0.011 0.001 TYR A 507 PHE 0.032 0.001 PHE B 701 TRP 0.019 0.002 TRP B 559 HIS 0.012 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00326 (13859) covalent geometry : angle 0.62474 (18779) SS BOND : bond 0.00378 ( 36) SS BOND : angle 1.03897 ( 72) hydrogen bonds : bond 0.03960 ( 313) hydrogen bonds : angle 7.29419 ( 825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.9657 (mmp) cc_final: 0.9453 (mmm) REVERT: A 376 LEU cc_start: 0.9534 (mp) cc_final: 0.9224 (pt) REVERT: A 709 LEU cc_start: 0.9744 (tt) cc_final: 0.9350 (mt) REVERT: A 831 MET cc_start: 0.9238 (tpt) cc_final: 0.9008 (tpt) REVERT: B 38 MET cc_start: 0.9222 (mmp) cc_final: 0.8631 (mmm) REVERT: B 553 MET cc_start: 0.9193 (mpp) cc_final: 0.8969 (mpp) REVERT: B 806 MET cc_start: 0.8916 (mpp) cc_final: 0.8467 (mpp) REVERT: B 852 TYR cc_start: 0.9355 (t80) cc_final: 0.8875 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1161 time to fit residues: 9.4058 Evaluate side-chains 44 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 46 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.035552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.023606 restraints weight = 235046.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.024371 restraints weight = 138335.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.024939 restraints weight = 97120.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.025339 restraints weight = 75189.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.025633 restraints weight = 62551.004| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13895 Z= 0.150 Angle : 0.612 9.309 18851 Z= 0.317 Chirality : 0.045 0.226 2037 Planarity : 0.005 0.094 2427 Dihedral : 5.103 24.759 1828 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.47 % Favored : 91.41 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.21), residues: 1642 helix: -0.59 (0.40), residues: 167 sheet: -0.56 (0.29), residues: 327 loop : -1.15 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 863 TYR 0.011 0.001 TYR A 562 PHE 0.032 0.002 PHE B 701 TRP 0.017 0.002 TRP B 559 HIS 0.009 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00334 (13859) covalent geometry : angle 0.61089 (18779) SS BOND : bond 0.00268 ( 36) SS BOND : angle 0.90268 ( 72) hydrogen bonds : bond 0.03859 ( 313) hydrogen bonds : angle 7.02660 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.43 seconds wall clock time: 41 minutes 23.84 seconds (2483.84 seconds total)