Starting phenix.real_space_refine on Thu Mar 5 01:47:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqp_14873/03_2026/7zqp_14873.map" } resolution = 3.6 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 11625 2.51 5 N 3078 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 18315 Number of models: 1 Model: "" Number of chains: 6 Chain: "d" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5777 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 23, 'TRANS': 696} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "j" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "h" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 328 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "c" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5777 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 23, 'TRANS': 696} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5777 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 23, 'TRANS': 696} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 4.36, per 1000 atoms: 0.24 Number of scatterers: 18315 At special positions: 0 Unit cell: (112.133, 116.186, 141.855, 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 27 16.00 O 3585 8.00 N 3078 7.00 C 11625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS d 316 " - pdb=" SG CYS d 327 " distance=2.03 Simple disulfide: pdb=" SG CYS c 316 " - pdb=" SG CYS c 327 " distance=2.03 Simple disulfide: pdb=" SG CYS b 316 " - pdb=" SG CYS b 327 " 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: 1.16 Conformation dependent library (CDL) restraints added in 719.2 milliseconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 34 sheets defined 22.4% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'd' and resid 5 through 15 Processing helix chain 'd' and resid 85 through 96 Processing helix chain 'd' and resid 162 through 167 removed outlier: 3.532A pdb=" N ASP d 166 " --> pdb=" O TYR d 163 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG d 167 " --> pdb=" O ASP d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 179 Processing helix chain 'd' and resid 318 through 325 Processing helix chain 'd' and resid 338 through 343 removed outlier: 4.170A pdb=" N ALA d 342 " --> pdb=" O MET d 338 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA d 343 " --> pdb=" O HIS d 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 338 through 343' Processing helix chain 'd' and resid 380 through 389 Processing helix chain 'd' and resid 392 through 399 Processing helix chain 'd' and resid 401 through 406 removed outlier: 3.844A pdb=" N TRP d 405 " --> pdb=" O PRO d 402 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP d 406 " --> pdb=" O GLU d 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 470 Processing helix chain 'd' and resid 478 through 482 removed outlier: 3.501A pdb=" N PHE d 482 " --> pdb=" O LEU d 479 " (cutoff:3.500A) Processing helix chain 'd' and resid 483 through 495 Processing helix chain 'd' and resid 502 through 506 Processing helix chain 'd' and resid 509 through 513 removed outlier: 3.504A pdb=" N GLY d 513 " --> pdb=" O ARG d 510 " (cutoff:3.500A) Processing helix chain 'd' and resid 536 through 549 removed outlier: 3.525A pdb=" N SER d 547 " --> pdb=" O GLY d 543 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE d 548 " --> pdb=" O ILE d 544 " (cutoff:3.500A) Processing helix chain 'd' and resid 587 through 592 Processing helix chain 'd' and resid 616 through 623 Processing helix chain 'd' and resid 639 through 654 Processing helix chain 'j' and resid 1105 through 1113 removed outlier: 4.120A pdb=" N LEU j1109 " --> pdb=" O SER j1105 " (cutoff:3.500A) Processing helix chain 'h' and resid 1105 through 1113 removed outlier: 4.089A pdb=" N LEU h1109 " --> pdb=" O SER h1105 " (cutoff:3.500A) Processing helix chain 'i' and resid 1105 through 1113 removed outlier: 4.108A pdb=" N LEU i1109 " --> pdb=" O SER i1105 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 15 Processing helix chain 'c' and resid 85 through 96 Processing helix chain 'c' and resid 161 through 167 removed outlier: 3.885A pdb=" N ARG c 167 " --> pdb=" O ASP c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 180 Processing helix chain 'c' and resid 318 through 325 removed outlier: 3.842A pdb=" N SER c 322 " --> pdb=" O ASP c 318 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP c 323 " --> pdb=" O GLU c 319 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR c 324 " --> pdb=" O THR c 320 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG c 325 " --> pdb=" O ASP c 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 318 through 325' Processing helix chain 'c' and resid 337 through 341 removed outlier: 3.649A pdb=" N ARG c 340 " --> pdb=" O THR c 337 " (cutoff:3.500A) Processing helix chain 'c' and resid 380 through 389 Processing helix chain 'c' and resid 392 through 399 Processing helix chain 'c' and resid 459 through 468 Processing helix chain 'c' and resid 478 through 482 Processing helix chain 'c' and resid 483 through 494 Processing helix chain 'c' and resid 509 through 513 removed outlier: 3.862A pdb=" N GLY c 513 " --> pdb=" O ARG c 510 " (cutoff:3.500A) Processing helix chain 'c' and resid 536 through 549 removed outlier: 3.541A pdb=" N SER c 547 " --> pdb=" O GLY c 543 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE c 548 " --> pdb=" O ILE c 544 " (cutoff:3.500A) Processing helix chain 'c' and resid 576 through 578 No H-bonds generated for 'chain 'c' and resid 576 through 578' Processing helix chain 'c' and resid 587 through 592 Processing helix chain 'c' and resid 616 through 623 Processing helix chain 'c' and resid 639 through 654 Processing helix chain 'c' and resid 665 through 669 Processing helix chain 'b' and resid 5 through 15 Processing helix chain 'b' and resid 85 through 96 Processing helix chain 'b' and resid 161 through 166 removed outlier: 3.544A pdb=" N ASP b 166 " --> pdb=" O TYR b 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 180 Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.669A pdb=" N GLN b 200 " --> pdb=" O PRO b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 326 Processing helix chain 'b' and resid 338 through 343 removed outlier: 4.361A pdb=" N ALA b 342 " --> pdb=" O MET b 338 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA b 343 " --> pdb=" O HIS b 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 338 through 343' Processing helix chain 'b' and resid 380 through 389 Processing helix chain 'b' and resid 392 through 399 Processing helix chain 'b' and resid 401 through 410 removed outlier: 4.034A pdb=" N TRP b 405 " --> pdb=" O PRO b 402 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP b 406 " --> pdb=" O GLU b 403 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER b 407 " --> pdb=" O TYR b 404 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG b 408 " --> pdb=" O TRP b 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS b 410 " --> pdb=" O SER b 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 469 Processing helix chain 'b' and resid 478 through 482 removed outlier: 3.649A pdb=" N PHE b 482 " --> pdb=" O LEU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 483 through 494 Processing helix chain 'b' and resid 502 through 506 removed outlier: 3.578A pdb=" N GLN b 506 " --> pdb=" O THR b 503 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 513 removed outlier: 3.509A pdb=" N GLY b 513 " --> pdb=" O ARG b 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 536 through 549 removed outlier: 3.588A pdb=" N SER b 547 " --> pdb=" O GLY b 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE b 548 " --> pdb=" O ILE b 544 " (cutoff:3.500A) Processing helix chain 'b' and resid 587 through 592 Processing helix chain 'b' and resid 603 through 606 Processing helix chain 'b' and resid 616 through 623 Processing helix chain 'b' and resid 639 through 654 Processing helix chain 'b' and resid 682 through 685 Processing sheet with id=AA1, first strand: chain 'd' and resid 37 through 42 removed outlier: 4.516A pdb=" N THR d 37 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS d 19 " --> pdb=" O ILE d 111 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY d 103 " --> pdb=" O GLU d 27 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE d 104 " --> pdb=" O ARG d 132 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG d 132 " --> pdb=" O ILE d 104 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE d 106 " --> pdb=" O PHE d 130 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY d 138 " --> pdb=" O ASP b 586 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP d 142 " --> pdb=" O LEU b 582 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN b 705 " --> pdb=" O VAL b 696 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL b 696 " --> pdb=" O ASN b 705 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL b 707 " --> pdb=" O ASP b 694 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 60 through 63 removed outlier: 7.207A pdb=" N VAL d 60 " --> pdb=" O THR d 82 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR d 82 " --> pdb=" O VAL d 60 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER d 62 " --> pdb=" O THR d 80 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL d 153 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY d 137 " --> pdb=" O ASN d 157 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER d 159 " --> pdb=" O ILE d 135 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE d 135 " --> pdb=" O SER d 159 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY d 138 " --> pdb=" O ASP b 586 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP d 142 " --> pdb=" O LEU b 582 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN b 705 " --> pdb=" O VAL b 696 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL b 696 " --> pdb=" O ASN b 705 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL b 707 " --> pdb=" O ASP b 694 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS b 687 " --> pdb=" O TYR b 681 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR b 681 " --> pdb=" O LYS b 687 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU b 571 " --> pdb=" O ALA b 678 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR b 680 " --> pdb=" O LEU b 571 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE b 573 " --> pdb=" O THR b 680 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 48 through 50 Processing sheet with id=AA4, first strand: chain 'd' and resid 66 through 69 removed outlier: 5.637A pdb=" N VAL d 693 " --> pdb=" O GLN d 709 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN d 709 " --> pdb=" O VAL d 693 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU d 660 " --> pdb=" O LEU d 708 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP c 142 " --> pdb=" O LEU d 582 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU c 129 " --> pdb=" O GLN c 108 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN c 108 " --> pdb=" O LEU c 129 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY c 103 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS c 19 " --> pdb=" O ILE c 111 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N LEU c 54 " --> pdb=" O TYR c 38 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR c 40 " --> pdb=" O LEU c 54 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG c 56 " --> pdb=" O TYR c 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 571 through 574 removed outlier: 6.362A pdb=" N LEU d 571 " --> pdb=" O ALA d 678 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR d 680 " --> pdb=" O LEU d 571 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE d 573 " --> pdb=" O THR d 680 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR d 681 " --> pdb=" O LYS d 687 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS d 687 " --> pdb=" O TYR d 681 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL d 693 " --> pdb=" O GLN d 709 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN d 709 " --> pdb=" O VAL d 693 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU d 660 " --> pdb=" O LEU d 708 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP c 142 " --> pdb=" O LEU d 582 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER c 62 " --> pdb=" O THR c 80 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR c 82 " --> pdb=" O VAL c 60 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL c 60 " --> pdb=" O THR c 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 216 through 220 Processing sheet with id=AA7, first strand: chain 'd' and resid 216 through 220 removed outlier: 3.514A pdb=" N ILE j1118 " --> pdb=" O VAL j1125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 225 through 226 removed outlier: 4.401A pdb=" N TYR d 225 " --> pdb=" O LYS d 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'd' and resid 266 through 267 Processing sheet with id=AB1, first strand: chain 'd' and resid 270 through 274 removed outlier: 3.536A pdb=" N ASP d 306 " --> pdb=" O GLU d 436 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN d 438 " --> pdb=" O PHE d 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE d 304 " --> pdb=" O GLN d 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 277 through 282 removed outlier: 6.413A pdb=" N ALA d 295 " --> pdb=" O PRO d 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE d 279 " --> pdb=" O VAL d 293 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA d 415 " --> pdb=" O PHE d 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 444 through 445 Processing sheet with id=AB4, first strand: chain 'd' and resid 550 through 554 Processing sheet with id=AB5, first strand: chain 'd' and resid 595 through 602 removed outlier: 3.857A pdb=" N LYS d 608 " --> pdb=" O ASP d 602 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL i1098 " --> pdb=" O SER d 611 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR d 613 " --> pdb=" O VAL i1098 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 1097 through 1099 removed outlier: 4.261A pdb=" N LYS b 608 " --> pdb=" O ASP b 602 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 1086 through 1092 removed outlier: 6.607A pdb=" N GLN h1087 " --> pdb=" O ASP b 254 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP b 256 " --> pdb=" O GLN h1087 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU h1089 " --> pdb=" O ASP b 256 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN b 258 " --> pdb=" O LEU h1089 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU h1091 " --> pdb=" O ASN b 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 1086 through 1092 removed outlier: 6.607A pdb=" N GLN h1087 " --> pdb=" O ASP b 254 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP b 256 " --> pdb=" O GLN h1087 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU h1089 " --> pdb=" O ASP b 256 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN b 258 " --> pdb=" O LEU h1089 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU h1091 " --> pdb=" O ASN b 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'h' and resid 1097 through 1099 Processing sheet with id=AC1, first strand: chain 'h' and resid 1118 through 1120 Processing sheet with id=AC2, first strand: chain 'i' and resid 1086 through 1087 removed outlier: 3.507A pdb=" N GLN i1087 " --> pdb=" O GLU c 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'i' and resid 1090 through 1092 removed outlier: 6.322A pdb=" N LEU i1091 " --> pdb=" O ASN c 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'i' and resid 1118 through 1119 Processing sheet with id=AC5, first strand: chain 'c' and resid 66 through 69 removed outlier: 7.285A pdb=" N PHE c 690 " --> pdb=" O TYR c 711 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR c 711 " --> pdb=" O PHE c 690 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL c 707 " --> pdb=" O ASP c 694 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL c 696 " --> pdb=" O ASN c 705 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN c 705 " --> pdb=" O VAL c 696 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY b 138 " --> pdb=" O ASP c 586 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE b 106 " --> pdb=" O PHE b 130 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG b 132 " --> pdb=" O ILE b 104 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE b 104 " --> pdb=" O ARG b 132 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY b 103 " --> pdb=" O GLU b 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS b 107 " --> pdb=" O LEU b 23 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS b 19 " --> pdb=" O ILE b 111 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR b 37 " --> pdb=" O LEU b 28 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N TYR b 38 " --> pdb=" O LEU b 54 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ARG b 56 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR b 40 " --> pdb=" O ARG b 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 571 through 574 removed outlier: 6.240A pdb=" N LEU c 571 " --> pdb=" O ALA c 678 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR c 680 " --> pdb=" O LEU c 571 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE c 573 " --> pdb=" O THR c 680 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR c 681 " --> pdb=" O LYS c 687 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYS c 687 " --> pdb=" O TYR c 681 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE c 690 " --> pdb=" O TYR c 711 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR c 711 " --> pdb=" O PHE c 690 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL c 707 " --> pdb=" O ASP c 694 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL c 696 " --> pdb=" O ASN c 705 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN c 705 " --> pdb=" O VAL c 696 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY b 138 " --> pdb=" O ASP c 586 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN b 157 " --> pdb=" O THR b 136 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY b 138 " --> pdb=" O THR b 155 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR b 155 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE b 140 " --> pdb=" O VAL b 153 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL b 153 " --> pdb=" O ILE b 140 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP b 142 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 151 " --> pdb=" O ASP b 142 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER b 62 " --> pdb=" O THR b 80 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR b 82 " --> pdb=" O VAL b 60 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL b 60 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 265 through 268 removed outlier: 3.987A pdb=" N THR c 529 " --> pdb=" O TYR c 268 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 271 through 274 Processing sheet with id=AC9, first strand: chain 'c' and resid 276 through 282 removed outlier: 6.620A pdb=" N VAL c 293 " --> pdb=" O ILE c 278 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA c 280 " --> pdb=" O TYR c 291 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR c 291 " --> pdb=" O ALA c 280 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR c 282 " --> pdb=" O ILE c 289 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE c 289 " --> pdb=" O THR c 282 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR c 422 " --> pdb=" O ASP c 365 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP c 365 " --> pdb=" O THR c 422 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 444 through 445 Processing sheet with id=AD2, first strand: chain 'c' and resid 550 through 555 removed outlier: 3.769A pdb=" N LEU c 555 " --> pdb=" O GLU c 558 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU c 558 " --> pdb=" O LEU c 555 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 266 through 268 Processing sheet with id=AD4, first strand: chain 'b' and resid 270 through 274 removed outlier: 6.553A pdb=" N GLN b 438 " --> pdb=" O PHE b 304 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE b 304 " --> pdb=" O GLN b 438 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 277 through 282 removed outlier: 6.569A pdb=" N VAL b 293 " --> pdb=" O ILE b 278 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA b 280 " --> pdb=" O TYR b 291 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR b 291 " --> pdb=" O ALA b 280 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR b 282 " --> pdb=" O ILE b 289 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE b 289 " --> pdb=" O THR b 282 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA b 415 " --> pdb=" O PHE b 296 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN b 355 " --> pdb=" O THR b 370 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 444 through 445 Processing sheet with id=AD7, first strand: chain 'b' and resid 550 through 555 removed outlier: 3.806A pdb=" N LEU b 555 " --> pdb=" O GLU b 558 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU b 558 " --> pdb=" O LEU b 555 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1758 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: 3.92 Time building geometry restraints manager: 1.57 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: 5984 1.34 - 1.46: 4376 1.46 - 1.58: 8300 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 18702 Sorted by residual: bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" N MET b 1 " pdb=" CA MET b 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 bond pdb=" N MET c 1 " pdb=" CA MET c 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N PRO c 119 " pdb=" CA PRO c 119 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.01e+00 bond pdb=" CA TYR d 409 " pdb=" C TYR d 409 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 9.98e-01 ... (remaining 18697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 24019 0.94 - 1.88: 1070 1.88 - 2.82: 135 2.82 - 3.76: 76 3.76 - 4.70: 14 Bond angle restraints: 25314 Sorted by residual: angle pdb=" N ILE d 278 " pdb=" CA ILE d 278 " pdb=" C ILE d 278 " ideal model delta sigma weight residual 111.90 109.64 2.26 8.10e-01 1.52e+00 7.81e+00 angle pdb=" CA GLY c 303 " pdb=" C GLY c 303 " pdb=" N PHE c 304 " ideal model delta sigma weight residual 114.23 116.35 -2.12 8.80e-01 1.29e+00 5.81e+00 angle pdb=" N VAL b 120 " pdb=" CA VAL b 120 " pdb=" C VAL b 120 " ideal model delta sigma weight residual 111.48 109.32 2.16 9.40e-01 1.13e+00 5.26e+00 angle pdb=" N TYR c 246 " pdb=" CA TYR c 246 " pdb=" C TYR c 246 " ideal model delta sigma weight residual 109.15 112.42 -3.27 1.44e+00 4.82e-01 5.17e+00 angle pdb=" N ASP c 318 " pdb=" CA ASP c 318 " pdb=" C ASP c 318 " ideal model delta sigma weight residual 108.34 111.29 -2.95 1.31e+00 5.83e-01 5.08e+00 ... (remaining 25309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 9908 16.62 - 33.25: 992 33.25 - 49.87: 190 49.87 - 66.50: 38 66.50 - 83.12: 11 Dihedral angle restraints: 11139 sinusoidal: 4485 harmonic: 6654 Sorted by residual: dihedral pdb=" CB CYS b 316 " pdb=" SG CYS b 316 " pdb=" SG CYS b 327 " pdb=" CB CYS b 327 " ideal model delta sinusoidal sigma weight residual 93.00 25.77 67.23 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS c 316 " pdb=" SG CYS c 316 " pdb=" SG CYS c 327 " pdb=" CB CYS c 327 " ideal model delta sinusoidal sigma weight residual 93.00 35.74 57.26 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS d 316 " pdb=" SG CYS d 316 " pdb=" SG CYS d 327 " pdb=" CB CYS d 327 " ideal model delta sinusoidal sigma weight residual 93.00 39.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 11136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1624 0.030 - 0.059: 778 0.059 - 0.089: 122 0.089 - 0.118: 183 0.118 - 0.148: 50 Chirality restraints: 2757 Sorted by residual: chirality pdb=" CA ILE b 430 " pdb=" N ILE b 430 " pdb=" C ILE b 430 " pdb=" CB ILE b 430 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE c 612 " pdb=" N ILE c 612 " pdb=" C ILE c 612 " pdb=" CB ILE c 612 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE c 530 " pdb=" N ILE c 530 " pdb=" C ILE c 530 " pdb=" CB ILE c 530 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2754 not shown) Planarity restraints: 3279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN d 189 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO d 190 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO d 190 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO d 190 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 225 " -0.016 2.00e-02 2.50e+03 9.81e-03 1.92e+00 pdb=" CG TYR d 225 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR d 225 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR d 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR d 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR d 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR d 225 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 225 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP b 516 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO b 517 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO b 517 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO b 517 " -0.019 5.00e-02 4.00e+02 ... (remaining 3276 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 274 2.62 - 3.19: 16594 3.19 - 3.76: 26502 3.76 - 4.33: 40520 4.33 - 4.90: 66363 Nonbonded interactions: 150253 Sorted by model distance: nonbonded pdb=" OG1 THR c 337 " pdb=" O GLN c 349 " model vdw 2.048 3.040 nonbonded pdb=" O LEU c 555 " pdb=" OG SER c 556 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASP c 302 " pdb=" NZ LYS c 441 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR b 308 " pdb=" OE2 GLU b 436 " model vdw 2.085 3.040 nonbonded pdb=" O LYS b 230 " pdb=" NH1 ARG b 238 " model vdw 2.115 3.120 ... (remaining 150248 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: 0.02 Found NCS groups: ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' } 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=0.00 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.280 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.003 0.031 18705 Z= 0.144 Angle : 0.480 4.698 25320 Z= 0.267 Chirality : 0.044 0.148 2757 Planarity : 0.003 0.053 3279 Dihedral : 13.614 83.120 6894 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.17), residues: 2277 helix: 0.75 (0.27), residues: 432 sheet: -0.45 (0.22), residues: 549 loop : -1.07 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 224 TYR 0.023 0.001 TYR c 409 PHE 0.008 0.001 PHE b 538 TRP 0.008 0.001 TRP d 369 HIS 0.003 0.001 HIS c 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (18702) covalent geometry : angle 0.47989 (25314) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.43084 ( 6) hydrogen bonds : bond 0.21883 ( 611) hydrogen bonds : angle 9.76463 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.681 Fit side-chains REVERT: d 1 MET cc_start: 0.6348 (ppp) cc_final: 0.5691 (ttp) REVERT: d 217 LYS cc_start: 0.7209 (mppt) cc_final: 0.6639 (ttmt) REVERT: d 251 LYS cc_start: 0.4916 (tttt) cc_final: 0.4589 (tttt) REVERT: d 281 ASP cc_start: 0.7995 (t0) cc_final: 0.7679 (t70) REVERT: d 465 MET cc_start: 0.7832 (mmm) cc_final: 0.7555 (mmm) REVERT: d 560 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7531 (mtp-110) REVERT: d 611 SER cc_start: 0.8046 (m) cc_final: 0.7814 (t) REVERT: d 612 ILE cc_start: 0.8198 (mm) cc_final: 0.7977 (mt) REVERT: d 631 GLN cc_start: 0.6569 (tp40) cc_final: 0.6296 (mm110) REVERT: d 633 SER cc_start: 0.8119 (t) cc_final: 0.7733 (p) REVERT: h 1095 GLN cc_start: 0.8026 (tp40) cc_final: 0.7730 (tp40) REVERT: i 1110 SER cc_start: 0.8898 (m) cc_final: 0.8566 (t) REVERT: c 1 MET cc_start: 0.6277 (ppp) cc_final: 0.5628 (ttt) REVERT: c 47 ASP cc_start: 0.8118 (m-30) cc_final: 0.7519 (p0) REVERT: c 87 ASP cc_start: 0.7393 (m-30) cc_final: 0.7145 (m-30) REVERT: c 143 ASN cc_start: 0.7774 (t0) cc_final: 0.7567 (t0) REVERT: c 251 LYS cc_start: 0.4855 (tttt) cc_final: 0.4652 (tttt) REVERT: c 338 MET cc_start: 0.7990 (ttp) cc_final: 0.7784 (ttp) REVERT: c 413 ASP cc_start: 0.8201 (m-30) cc_final: 0.7934 (m-30) REVERT: c 508 TYR cc_start: 0.8027 (m-80) cc_final: 0.7758 (m-80) REVERT: c 554 ASN cc_start: 0.8470 (t0) cc_final: 0.7786 (t0) REVERT: b 51 ASN cc_start: 0.8091 (m-40) cc_final: 0.7188 (m-40) REVERT: b 62 SER cc_start: 0.8817 (p) cc_final: 0.8554 (p) REVERT: b 143 ASN cc_start: 0.7566 (m110) cc_final: 0.7343 (t0) REVERT: b 217 LYS cc_start: 0.7348 (ttpt) cc_final: 0.6904 (ttmt) REVERT: b 251 LYS cc_start: 0.4939 (tttt) cc_final: 0.3909 (tttt) REVERT: b 306 ASP cc_start: 0.7548 (t70) cc_final: 0.7225 (t0) REVERT: b 330 ARG cc_start: 0.6886 (mtt90) cc_final: 0.6538 (mtt-85) REVERT: b 398 ASN cc_start: 0.7053 (t0) cc_final: 0.6844 (t0) REVERT: b 465 MET cc_start: 0.8183 (tpp) cc_final: 0.7749 (mmm) REVERT: b 499 GLU cc_start: 0.7903 (mp0) cc_final: 0.7609 (mt-10) REVERT: b 529 THR cc_start: 0.8334 (m) cc_final: 0.7885 (p) REVERT: b 535 GLU cc_start: 0.7560 (mp0) cc_final: 0.7287 (mm-30) REVERT: b 566 TYR cc_start: 0.7819 (t80) cc_final: 0.7432 (t80) REVERT: b 608 LYS cc_start: 0.8214 (mttm) cc_final: 0.7756 (mttt) REVERT: b 612 ILE cc_start: 0.7712 (mt) cc_final: 0.7482 (mt) REVERT: b 636 ASN cc_start: 0.8095 (m-40) cc_final: 0.7871 (m-40) REVERT: b 641 TYR cc_start: 0.7647 (m-80) cc_final: 0.7389 (m-80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1334 time to fit residues: 48.1152 Evaluate side-chains 152 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN d 591 ASN d 622 GLN c 51 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 528 ASN b 145 ASN b 506 GLN b 528 ASN b 709 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.087152 restraints weight = 28557.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.088938 restraints weight = 16797.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.090089 restraints weight = 11839.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090668 restraints weight = 9519.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091199 restraints weight = 8423.851| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18705 Z= 0.182 Angle : 0.557 11.063 25320 Z= 0.302 Chirality : 0.046 0.194 2757 Planarity : 0.004 0.047 3279 Dihedral : 4.603 25.412 2520 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.70 % Allowed : 6.71 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.17), residues: 2277 helix: 0.62 (0.26), residues: 435 sheet: -0.53 (0.22), residues: 576 loop : -0.97 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 644 TYR 0.016 0.002 TYR b 416 PHE 0.013 0.002 PHE d 662 TRP 0.012 0.001 TRP d 156 HIS 0.005 0.001 HIS c 207 Details of bonding type rmsd covalent geometry : bond 0.00421 (18702) covalent geometry : angle 0.55712 (25314) SS BOND : bond 0.00485 ( 3) SS BOND : angle 0.72703 ( 6) hydrogen bonds : bond 0.04208 ( 611) hydrogen bonds : angle 6.50105 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.775 Fit side-chains REVERT: d 1 MET cc_start: 0.6407 (ppp) cc_final: 0.5788 (ttp) REVERT: d 125 ASP cc_start: 0.7310 (m-30) cc_final: 0.7097 (m-30) REVERT: d 217 LYS cc_start: 0.7339 (mppt) cc_final: 0.6753 (ttmt) REVERT: d 436 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6294 (mt-10) REVERT: d 633 SER cc_start: 0.7828 (t) cc_final: 0.7431 (p) REVERT: h 1090 THR cc_start: 0.8016 (m) cc_final: 0.7497 (p) REVERT: h 1095 GLN cc_start: 0.8203 (tp40) cc_final: 0.7926 (tp40) REVERT: c 47 ASP cc_start: 0.7979 (m-30) cc_final: 0.7566 (p0) REVERT: c 338 MET cc_start: 0.8194 (ttp) cc_final: 0.7982 (ttp) REVERT: c 436 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6074 (mt-10) REVERT: c 438 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: c 448 ASP cc_start: 0.7304 (p0) cc_final: 0.7043 (p0) REVERT: c 554 ASN cc_start: 0.8583 (t0) cc_final: 0.7921 (t0) REVERT: b 143 ASN cc_start: 0.7640 (m110) cc_final: 0.7400 (t0) REVERT: b 217 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7011 (ttmt) REVERT: b 266 VAL cc_start: 0.8857 (t) cc_final: 0.8561 (p) REVERT: b 465 MET cc_start: 0.8187 (tpp) cc_final: 0.7933 (mmm) REVERT: b 566 TYR cc_start: 0.7817 (t80) cc_final: 0.7544 (t80) REVERT: b 608 LYS cc_start: 0.7721 (mttm) cc_final: 0.7437 (mttt) outliers start: 14 outliers final: 12 residues processed: 169 average time/residue: 0.1317 time to fit residues: 34.9030 Evaluate side-chains 150 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 578 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 400 ASN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 709 GLN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 228 GLN b 636 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089163 restraints weight = 29168.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089833 restraints weight = 19428.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.090556 restraints weight = 13999.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.091196 restraints weight = 12131.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.091230 restraints weight = 10785.033| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 18705 Z= 0.299 Angle : 0.657 12.908 25320 Z= 0.353 Chirality : 0.050 0.229 2757 Planarity : 0.005 0.044 3279 Dihedral : 5.277 25.753 2520 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.79 % Allowed : 10.68 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.17), residues: 2277 helix: 0.01 (0.24), residues: 435 sheet: -0.62 (0.22), residues: 549 loop : -1.23 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 330 TYR 0.021 0.002 TYR b 416 PHE 0.019 0.002 PHE c 296 TRP 0.011 0.002 TRP d 156 HIS 0.007 0.002 HIS c 207 Details of bonding type rmsd covalent geometry : bond 0.00703 (18702) covalent geometry : angle 0.65694 (25314) SS BOND : bond 0.00708 ( 3) SS BOND : angle 1.03355 ( 6) hydrogen bonds : bond 0.04702 ( 611) hydrogen bonds : angle 6.41693 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.713 Fit side-chains REVERT: d 217 LYS cc_start: 0.7222 (mppt) cc_final: 0.6754 (ttmt) REVERT: d 256 ASP cc_start: 0.6907 (t0) cc_final: 0.6368 (t0) REVERT: d 448 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6725 (p0) REVERT: d 612 ILE cc_start: 0.8150 (mt) cc_final: 0.7923 (mt) REVERT: d 633 SER cc_start: 0.7818 (t) cc_final: 0.7525 (p) REVERT: j 1108 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7903 (mt-10) REVERT: h 1095 GLN cc_start: 0.8135 (tp40) cc_final: 0.7896 (tp40) REVERT: i 1102 MET cc_start: 0.7981 (mtt) cc_final: 0.7736 (mtt) REVERT: c 47 ASP cc_start: 0.8142 (m-30) cc_final: 0.7912 (p0) REVERT: c 436 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6254 (mt-10) REVERT: c 438 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: c 448 ASP cc_start: 0.7353 (p0) cc_final: 0.7036 (p0) REVERT: c 605 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (pp) REVERT: b 143 ASN cc_start: 0.7627 (m110) cc_final: 0.7143 (t0) REVERT: b 198 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: b 217 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7295 (ttmt) REVERT: b 465 MET cc_start: 0.8337 (tpp) cc_final: 0.8058 (mmm) REVERT: b 566 TYR cc_start: 0.7739 (t80) cc_final: 0.7429 (t80) REVERT: b 608 LYS cc_start: 0.7965 (mttm) cc_final: 0.7369 (mttt) REVERT: b 664 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8628 (m) outliers start: 36 outliers final: 25 residues processed: 174 average time/residue: 0.1294 time to fit residues: 35.3759 Evaluate side-chains 154 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 437 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 450 THR Chi-restraints excluded: chain d residue 494 LEU Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 605 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain c residue 709 GLN Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 411 LEU Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 50.0000 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN i1095 GLN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 68 GLN ** 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 = 0.3248 r_free = 0.3248 target = 0.109707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.089528 restraints weight = 29096.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.090880 restraints weight = 17980.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091578 restraints weight = 12951.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.092117 restraints weight = 10315.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.092175 restraints weight = 9331.010| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18705 Z= 0.218 Angle : 0.569 11.139 25320 Z= 0.308 Chirality : 0.047 0.192 2757 Planarity : 0.004 0.052 3279 Dihedral : 5.033 25.561 2520 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.33 % Allowed : 12.72 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.29 (0.17), residues: 2277 helix: 0.11 (0.25), residues: 435 sheet: -0.60 (0.22), residues: 543 loop : -1.31 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 330 TYR 0.016 0.002 TYR b 416 PHE 0.017 0.002 PHE c 296 TRP 0.010 0.001 TRP d 156 HIS 0.004 0.001 HIS c 207 Details of bonding type rmsd covalent geometry : bond 0.00512 (18702) covalent geometry : angle 0.56844 (25314) SS BOND : bond 0.00616 ( 3) SS BOND : angle 0.92071 ( 6) hydrogen bonds : bond 0.03939 ( 611) hydrogen bonds : angle 6.08213 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.700 Fit side-chains REVERT: d 217 LYS cc_start: 0.7196 (mppt) cc_final: 0.6650 (ttmt) REVERT: d 256 ASP cc_start: 0.6842 (t0) cc_final: 0.6328 (t0) REVERT: d 448 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6874 (p0) REVERT: d 612 ILE cc_start: 0.8149 (mt) cc_final: 0.7888 (mt) REVERT: d 633 SER cc_start: 0.7825 (t) cc_final: 0.7539 (p) REVERT: i 1102 MET cc_start: 0.7984 (mtt) cc_final: 0.7714 (mtt) REVERT: c 47 ASP cc_start: 0.8149 (m-30) cc_final: 0.7913 (p0) REVERT: c 306 ASP cc_start: 0.7857 (t0) cc_final: 0.7614 (t0) REVERT: c 338 MET cc_start: 0.8192 (ttp) cc_final: 0.7937 (ttp) REVERT: c 438 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7016 (mt0) REVERT: c 448 ASP cc_start: 0.7495 (p0) cc_final: 0.7155 (p0) REVERT: c 579 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8316 (m-10) REVERT: c 605 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7346 (pp) REVERT: b 143 ASN cc_start: 0.7609 (m110) cc_final: 0.7067 (t0) REVERT: b 198 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: b 217 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7251 (ttmt) REVERT: b 266 VAL cc_start: 0.8902 (t) cc_final: 0.8623 (p) REVERT: b 465 MET cc_start: 0.8357 (tpp) cc_final: 0.8069 (mmm) REVERT: b 499 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: b 608 LYS cc_start: 0.7938 (mttm) cc_final: 0.7279 (mttt) REVERT: b 632 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7423 (mp) REVERT: b 664 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8655 (m) outliers start: 47 outliers final: 28 residues processed: 175 average time/residue: 0.1155 time to fit residues: 32.7790 Evaluate side-chains 164 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 605 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 632 LEU Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 196 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 438 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.091603 restraints weight = 28781.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.092117 restraints weight = 18456.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092554 restraints weight = 14899.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092778 restraints weight = 12545.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092892 restraints weight = 12315.569| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18705 Z= 0.172 Angle : 0.522 9.835 25320 Z= 0.283 Chirality : 0.046 0.178 2757 Planarity : 0.003 0.041 3279 Dihedral : 4.811 25.412 2520 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.88 % Allowed : 13.31 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.17), residues: 2277 helix: 0.29 (0.25), residues: 435 sheet: -0.52 (0.23), residues: 540 loop : -1.31 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 325 TYR 0.016 0.002 TYR d 308 PHE 0.016 0.002 PHE c 296 TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 Details of bonding type rmsd covalent geometry : bond 0.00400 (18702) covalent geometry : angle 0.52154 (25314) SS BOND : bond 0.00492 ( 3) SS BOND : angle 0.73618 ( 6) hydrogen bonds : bond 0.03527 ( 611) hydrogen bonds : angle 5.81158 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.708 Fit side-chains REVERT: d 1 MET cc_start: 0.6375 (ppp) cc_final: 0.6053 (ttp) REVERT: d 217 LYS cc_start: 0.7114 (mppt) cc_final: 0.6627 (ttmt) REVERT: d 306 ASP cc_start: 0.7904 (t70) cc_final: 0.7556 (t70) REVERT: d 448 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6809 (p0) REVERT: d 612 ILE cc_start: 0.8243 (mt) cc_final: 0.7976 (mt) REVERT: d 633 SER cc_start: 0.7883 (t) cc_final: 0.7587 (p) REVERT: d 646 TYR cc_start: 0.8294 (t80) cc_final: 0.8055 (t80) REVERT: h 1090 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7619 (p) REVERT: i 1095 GLN cc_start: 0.7812 (tp40) cc_final: 0.7554 (tp-100) REVERT: i 1102 MET cc_start: 0.7933 (mtt) cc_final: 0.7671 (mtt) REVERT: i 1120 ASN cc_start: 0.7169 (t0) cc_final: 0.6901 (t0) REVERT: c 47 ASP cc_start: 0.8035 (m-30) cc_final: 0.7658 (p0) REVERT: c 306 ASP cc_start: 0.7725 (t0) cc_final: 0.7446 (t0) REVERT: c 338 MET cc_start: 0.8217 (ttp) cc_final: 0.7951 (ttp) REVERT: c 438 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: c 448 ASP cc_start: 0.7351 (p0) cc_final: 0.7136 (p0) REVERT: c 480 ASP cc_start: 0.7236 (p0) cc_final: 0.7031 (p0) REVERT: c 579 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: c 605 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7507 (pp) REVERT: b 51 ASN cc_start: 0.7627 (m110) cc_final: 0.7228 (m110) REVERT: b 143 ASN cc_start: 0.7605 (m110) cc_final: 0.7076 (t0) REVERT: b 217 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6993 (ttmt) REVERT: b 465 MET cc_start: 0.8320 (tpp) cc_final: 0.8087 (mmm) REVERT: b 518 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.7024 (mm) REVERT: b 554 ASN cc_start: 0.8399 (t0) cc_final: 0.8067 (t0) REVERT: b 608 LYS cc_start: 0.7909 (mttm) cc_final: 0.7240 (mttt) REVERT: b 632 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7393 (mp) REVERT: b 664 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8617 (m) outliers start: 58 outliers final: 42 residues processed: 187 average time/residue: 0.1158 time to fit residues: 34.9293 Evaluate side-chains 180 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 630 LEU Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 600 LEU Chi-restraints excluded: chain c residue 605 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 411 LEU Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 450 THR Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 518 LEU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 632 LEU Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 203 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 GLN b 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091188 restraints weight = 28687.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091971 restraints weight = 18742.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092273 restraints weight = 13574.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092674 restraints weight = 12997.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092932 restraints weight = 10848.631| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18705 Z= 0.233 Angle : 0.578 11.038 25320 Z= 0.312 Chirality : 0.047 0.198 2757 Planarity : 0.004 0.045 3279 Dihedral : 5.056 26.153 2520 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 14.21 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.16), residues: 2277 helix: 0.09 (0.25), residues: 435 sheet: -0.63 (0.23), residues: 528 loop : -1.42 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 325 TYR 0.016 0.002 TYR b 416 PHE 0.019 0.002 PHE c 296 TRP 0.010 0.001 TRP d 156 HIS 0.005 0.001 HIS d 107 Details of bonding type rmsd covalent geometry : bond 0.00549 (18702) covalent geometry : angle 0.57832 (25314) SS BOND : bond 0.00599 ( 3) SS BOND : angle 0.81197 ( 6) hydrogen bonds : bond 0.03880 ( 611) hydrogen bonds : angle 5.93294 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 0.686 Fit side-chains REVERT: d 1 MET cc_start: 0.6416 (ppp) cc_final: 0.6113 (ttp) REVERT: d 149 ILE cc_start: 0.7898 (mm) cc_final: 0.7532 (mt) REVERT: d 217 LYS cc_start: 0.7120 (mppt) cc_final: 0.6647 (ttmt) REVERT: d 448 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6987 (p0) REVERT: d 612 ILE cc_start: 0.8247 (mt) cc_final: 0.7994 (mt) REVERT: d 633 SER cc_start: 0.7822 (t) cc_final: 0.7505 (p) REVERT: j 1090 THR cc_start: 0.7646 (m) cc_final: 0.7157 (p) REVERT: h 1090 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7581 (p) REVERT: i 1095 GLN cc_start: 0.7735 (tp40) cc_final: 0.7453 (tp-100) REVERT: i 1102 MET cc_start: 0.7997 (mtt) cc_final: 0.7734 (mtt) REVERT: c 47 ASP cc_start: 0.8059 (m-30) cc_final: 0.7695 (p0) REVERT: c 306 ASP cc_start: 0.7748 (t0) cc_final: 0.7469 (t0) REVERT: c 338 MET cc_start: 0.8239 (ttp) cc_final: 0.7947 (ttp) REVERT: c 438 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: c 448 ASP cc_start: 0.7312 (p0) cc_final: 0.7100 (p0) REVERT: c 579 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: c 605 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7512 (pp) REVERT: b 51 ASN cc_start: 0.7458 (m110) cc_final: 0.7180 (m110) REVERT: b 143 ASN cc_start: 0.7659 (m110) cc_final: 0.6982 (t0) REVERT: b 217 LYS cc_start: 0.7413 (ttpt) cc_final: 0.7018 (ttmt) REVERT: b 266 VAL cc_start: 0.8898 (t) cc_final: 0.8622 (p) REVERT: b 465 MET cc_start: 0.8362 (tpp) cc_final: 0.8131 (mmm) REVERT: b 499 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: b 554 ASN cc_start: 0.8177 (t0) cc_final: 0.7630 (t0) REVERT: b 608 LYS cc_start: 0.7884 (mttm) cc_final: 0.7263 (mttt) REVERT: b 632 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7430 (mp) REVERT: b 664 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8639 (m) outliers start: 64 outliers final: 47 residues processed: 190 average time/residue: 0.1236 time to fit residues: 37.7781 Evaluate side-chains 186 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 630 LEU Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 600 LEU Chi-restraints excluded: chain c residue 605 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 411 LEU Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 632 LEU Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 0.0870 chunk 90 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 360 ASN b 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.091008 restraints weight = 28766.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.091686 restraints weight = 17411.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092700 restraints weight = 14729.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093364 restraints weight = 10731.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.093465 restraints weight = 9921.203| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18705 Z= 0.168 Angle : 0.517 9.267 25320 Z= 0.281 Chirality : 0.046 0.177 2757 Planarity : 0.003 0.039 3279 Dihedral : 4.783 25.486 2520 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.03 % Allowed : 15.10 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2277 helix: 0.09 (0.25), residues: 456 sheet: -0.34 (0.24), residues: 492 loop : -1.51 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 325 TYR 0.013 0.001 TYR c 646 PHE 0.018 0.002 PHE c 296 TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 Details of bonding type rmsd covalent geometry : bond 0.00394 (18702) covalent geometry : angle 0.51684 (25314) SS BOND : bond 0.00474 ( 3) SS BOND : angle 0.73350 ( 6) hydrogen bonds : bond 0.03393 ( 611) hydrogen bonds : angle 5.68937 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.730 Fit side-chains REVERT: d 1 MET cc_start: 0.6403 (ppp) cc_final: 0.6020 (ttp) REVERT: d 149 ILE cc_start: 0.7854 (mm) cc_final: 0.7502 (mt) REVERT: d 217 LYS cc_start: 0.7045 (mppt) cc_final: 0.6591 (ttmt) REVERT: d 306 ASP cc_start: 0.7941 (t70) cc_final: 0.7474 (t70) REVERT: d 633 SER cc_start: 0.7825 (t) cc_final: 0.7507 (p) REVERT: j 1090 THR cc_start: 0.7611 (m) cc_final: 0.7102 (p) REVERT: h 1090 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7684 (p) REVERT: i 1095 GLN cc_start: 0.7758 (tp40) cc_final: 0.7459 (tp-100) REVERT: i 1102 MET cc_start: 0.7959 (mtt) cc_final: 0.7692 (mtt) REVERT: c 47 ASP cc_start: 0.8047 (m-30) cc_final: 0.7678 (p0) REVERT: c 219 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6662 (mm-40) REVERT: c 306 ASP cc_start: 0.7768 (t0) cc_final: 0.7387 (t0) REVERT: c 308 TYR cc_start: 0.7636 (m-80) cc_final: 0.7395 (m-80) REVERT: c 338 MET cc_start: 0.8164 (ttp) cc_final: 0.7847 (ttp) REVERT: c 448 ASP cc_start: 0.7273 (p0) cc_final: 0.7045 (p0) REVERT: c 465 MET cc_start: 0.8416 (tpp) cc_final: 0.8022 (mmm) REVERT: c 579 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8314 (m-10) REVERT: b 51 ASN cc_start: 0.7430 (m110) cc_final: 0.7203 (m110) REVERT: b 143 ASN cc_start: 0.7609 (m110) cc_final: 0.7024 (t0) REVERT: b 217 LYS cc_start: 0.7371 (ttpt) cc_final: 0.6968 (ttmt) REVERT: b 266 VAL cc_start: 0.8808 (t) cc_final: 0.8558 (p) REVERT: b 436 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6316 (mt-10) REVERT: b 465 MET cc_start: 0.8285 (tpp) cc_final: 0.8071 (mmm) REVERT: b 499 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: b 554 ASN cc_start: 0.8143 (t0) cc_final: 0.7743 (t0) REVERT: b 608 LYS cc_start: 0.7873 (mttm) cc_final: 0.7211 (mttt) REVERT: b 632 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7435 (mp) REVERT: b 664 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8605 (m) outliers start: 61 outliers final: 46 residues processed: 189 average time/residue: 0.1238 time to fit residues: 37.7951 Evaluate side-chains 183 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 630 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 411 LEU Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 632 LEU Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 41 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 151 optimal weight: 0.0030 chunk 1 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 569 ASN i1120 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.089992 restraints weight = 29043.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.091112 restraints weight = 17944.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091883 restraints weight = 12992.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.092438 restraints weight = 10911.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092474 restraints weight = 9870.274| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18705 Z= 0.232 Angle : 0.576 10.273 25320 Z= 0.310 Chirality : 0.047 0.197 2757 Planarity : 0.004 0.039 3279 Dihedral : 5.031 26.011 2520 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.93 % Allowed : 15.65 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.17), residues: 2277 helix: 0.13 (0.25), residues: 435 sheet: -0.44 (0.23), residues: 498 loop : -1.52 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 325 TYR 0.016 0.002 TYR b 416 PHE 0.020 0.002 PHE c 296 TRP 0.009 0.001 TRP d 156 HIS 0.005 0.001 HIS d 107 Details of bonding type rmsd covalent geometry : bond 0.00547 (18702) covalent geometry : angle 0.57544 (25314) SS BOND : bond 0.00650 ( 3) SS BOND : angle 1.21343 ( 6) hydrogen bonds : bond 0.03787 ( 611) hydrogen bonds : angle 5.85104 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.698 Fit side-chains REVERT: d 1 MET cc_start: 0.6356 (ppp) cc_final: 0.6045 (ttp) REVERT: d 149 ILE cc_start: 0.7921 (mm) cc_final: 0.7537 (mt) REVERT: d 217 LYS cc_start: 0.7065 (mppt) cc_final: 0.6633 (ttmt) REVERT: d 306 ASP cc_start: 0.7968 (t70) cc_final: 0.7589 (t70) REVERT: d 612 ILE cc_start: 0.8252 (mt) cc_final: 0.7969 (mt) REVERT: d 633 SER cc_start: 0.7819 (t) cc_final: 0.7517 (p) REVERT: j 1090 THR cc_start: 0.7804 (m) cc_final: 0.7229 (p) REVERT: h 1090 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7603 (p) REVERT: i 1095 GLN cc_start: 0.7750 (tp40) cc_final: 0.7534 (tp-100) REVERT: i 1102 MET cc_start: 0.7932 (mtt) cc_final: 0.7681 (mtt) REVERT: c 47 ASP cc_start: 0.8049 (m-30) cc_final: 0.7693 (p0) REVERT: c 219 GLN cc_start: 0.6839 (mm-40) cc_final: 0.6570 (mm-40) REVERT: c 306 ASP cc_start: 0.7793 (t0) cc_final: 0.7430 (t0) REVERT: c 308 TYR cc_start: 0.7675 (m-80) cc_final: 0.7442 (m-80) REVERT: c 338 MET cc_start: 0.8150 (ttp) cc_final: 0.7819 (ttp) REVERT: c 406 ASP cc_start: 0.7301 (t0) cc_final: 0.7023 (t70) REVERT: c 448 ASP cc_start: 0.7256 (p0) cc_final: 0.7027 (p0) REVERT: c 579 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: b 143 ASN cc_start: 0.7643 (m110) cc_final: 0.7004 (t0) REVERT: b 266 VAL cc_start: 0.8892 (t) cc_final: 0.8611 (p) REVERT: b 465 MET cc_start: 0.8331 (tpp) cc_final: 0.8127 (mmm) REVERT: b 499 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: b 554 ASN cc_start: 0.8174 (t0) cc_final: 0.7780 (t0) REVERT: b 608 LYS cc_start: 0.7866 (mttm) cc_final: 0.7204 (mttt) REVERT: b 632 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7474 (mp) REVERT: b 664 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8641 (m) REVERT: b 675 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7599 (m-30) outliers start: 59 outliers final: 51 residues processed: 180 average time/residue: 0.1178 time to fit residues: 34.3983 Evaluate side-chains 183 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 630 LEU Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain i residue 1109 LEU Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 630 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 411 LEU Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 600 LEU Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 632 LEU Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 569 ASN d 591 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 591 ASN b 51 ASN b 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092256 restraints weight = 28538.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.093342 restraints weight = 18416.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.094080 restraints weight = 12593.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094712 restraints weight = 10805.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094734 restraints weight = 9931.878| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18705 Z= 0.114 Angle : 0.483 7.794 25320 Z= 0.263 Chirality : 0.045 0.167 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.546 25.126 2520 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.33 % Allowed : 16.44 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.17), residues: 2277 helix: 0.29 (0.25), residues: 456 sheet: -0.30 (0.24), residues: 486 loop : -1.45 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 644 TYR 0.017 0.001 TYR j1088 PHE 0.016 0.001 PHE c 296 TRP 0.011 0.001 TRP b 369 HIS 0.004 0.001 HIS b 339 Details of bonding type rmsd covalent geometry : bond 0.00258 (18702) covalent geometry : angle 0.48248 (25314) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.84967 ( 6) hydrogen bonds : bond 0.03043 ( 611) hydrogen bonds : angle 5.45875 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.678 Fit side-chains REVERT: d 1 MET cc_start: 0.6332 (ppp) cc_final: 0.6051 (ttp) REVERT: d 149 ILE cc_start: 0.7908 (mm) cc_final: 0.7535 (mt) REVERT: d 217 LYS cc_start: 0.7009 (mppt) cc_final: 0.6571 (ttmt) REVERT: d 306 ASP cc_start: 0.7718 (t70) cc_final: 0.7312 (t70) REVERT: d 633 SER cc_start: 0.7806 (t) cc_final: 0.7484 (p) REVERT: j 1090 THR cc_start: 0.7578 (m) cc_final: 0.7095 (p) REVERT: h 1090 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7530 (p) REVERT: i 1095 GLN cc_start: 0.7832 (tp40) cc_final: 0.7546 (tp-100) REVERT: i 1102 MET cc_start: 0.7912 (mtt) cc_final: 0.7667 (mtt) REVERT: c 1 MET cc_start: 0.6617 (ppp) cc_final: 0.6347 (ttp) REVERT: c 18 LEU cc_start: 0.8288 (mt) cc_final: 0.8087 (mt) REVERT: c 47 ASP cc_start: 0.8034 (m-30) cc_final: 0.7678 (p0) REVERT: c 166 ASP cc_start: 0.6437 (m-30) cc_final: 0.6222 (m-30) REVERT: c 251 LYS cc_start: 0.5024 (tttt) cc_final: 0.4794 (tttt) REVERT: c 306 ASP cc_start: 0.7728 (t0) cc_final: 0.7344 (t0) REVERT: c 308 TYR cc_start: 0.7654 (m-80) cc_final: 0.7333 (m-80) REVERT: c 338 MET cc_start: 0.8150 (ttp) cc_final: 0.7842 (ttp) REVERT: c 406 ASP cc_start: 0.7221 (t0) cc_final: 0.7009 (t70) REVERT: c 448 ASP cc_start: 0.7221 (p0) cc_final: 0.6985 (p0) REVERT: c 465 MET cc_start: 0.8396 (tpp) cc_final: 0.8054 (mmm) REVERT: c 554 ASN cc_start: 0.8491 (t0) cc_final: 0.7908 (t0) REVERT: c 579 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8225 (m-10) REVERT: c 611 SER cc_start: 0.7367 (m) cc_final: 0.6977 (t) REVERT: b 143 ASN cc_start: 0.7557 (m110) cc_final: 0.7039 (t0) REVERT: b 436 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6000 (mt-10) REVERT: b 499 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: b 554 ASN cc_start: 0.7983 (t0) cc_final: 0.7500 (t0) REVERT: b 608 LYS cc_start: 0.7811 (mttm) cc_final: 0.7158 (mttt) REVERT: b 664 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8566 (m) REVERT: b 675 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7506 (m-30) outliers start: 47 outliers final: 37 residues processed: 182 average time/residue: 0.1228 time to fit residues: 35.9730 Evaluate side-chains 175 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 630 LEU Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 630 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 159 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 151 optimal weight: 0.1980 chunk 182 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 398 ASN b 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095827 restraints weight = 27841.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.097682 restraints weight = 16601.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098872 restraints weight = 11807.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099662 restraints weight = 9535.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099993 restraints weight = 8318.506| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18705 Z= 0.121 Angle : 0.480 7.651 25320 Z= 0.261 Chirality : 0.045 0.161 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.457 25.129 2520 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 16.64 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.17), residues: 2277 helix: 0.37 (0.25), residues: 456 sheet: -0.24 (0.24), residues: 486 loop : -1.40 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 330 TYR 0.016 0.001 TYR j1088 PHE 0.016 0.001 PHE c 296 TRP 0.011 0.001 TRP b 369 HIS 0.005 0.001 HIS b 339 Details of bonding type rmsd covalent geometry : bond 0.00280 (18702) covalent geometry : angle 0.48009 (25314) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.67060 ( 6) hydrogen bonds : bond 0.03052 ( 611) hydrogen bonds : angle 5.35349 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.613 Fit side-chains REVERT: d 1 MET cc_start: 0.6320 (ppp) cc_final: 0.6059 (ttp) REVERT: d 149 ILE cc_start: 0.7897 (mm) cc_final: 0.7536 (mt) REVERT: d 217 LYS cc_start: 0.7021 (mppt) cc_final: 0.6567 (ttmt) REVERT: d 306 ASP cc_start: 0.7908 (t70) cc_final: 0.7529 (t70) REVERT: d 314 MET cc_start: 0.6601 (mtm) cc_final: 0.6337 (mtp) REVERT: d 413 ASP cc_start: 0.7809 (m-30) cc_final: 0.7540 (m-30) REVERT: d 443 LYS cc_start: 0.7975 (mttp) cc_final: 0.7610 (mtmm) REVERT: d 560 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7514 (mtp-110) REVERT: d 633 SER cc_start: 0.7774 (t) cc_final: 0.7427 (p) REVERT: j 1090 THR cc_start: 0.7573 (m) cc_final: 0.7101 (p) REVERT: h 1090 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7448 (p) REVERT: i 1095 GLN cc_start: 0.7789 (tp40) cc_final: 0.7519 (tp-100) REVERT: i 1102 MET cc_start: 0.7820 (mtt) cc_final: 0.7565 (mtt) REVERT: c 1 MET cc_start: 0.6604 (ppp) cc_final: 0.6360 (ttp) REVERT: c 47 ASP cc_start: 0.8063 (m-30) cc_final: 0.7676 (p0) REVERT: c 166 ASP cc_start: 0.6566 (m-30) cc_final: 0.6321 (m-30) REVERT: c 219 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6539 (mm-40) REVERT: c 251 LYS cc_start: 0.5024 (tttt) cc_final: 0.4807 (tttt) REVERT: c 306 ASP cc_start: 0.7703 (t0) cc_final: 0.7317 (t0) REVERT: c 308 TYR cc_start: 0.7634 (m-80) cc_final: 0.7355 (m-80) REVERT: c 338 MET cc_start: 0.8154 (ttp) cc_final: 0.7851 (ttp) REVERT: c 448 ASP cc_start: 0.7158 (p0) cc_final: 0.6909 (p0) REVERT: c 465 MET cc_start: 0.8398 (tpp) cc_final: 0.8074 (mmm) REVERT: c 554 ASN cc_start: 0.8501 (t0) cc_final: 0.7905 (t0) REVERT: c 579 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: c 611 SER cc_start: 0.7373 (m) cc_final: 0.6976 (t) REVERT: b 143 ASN cc_start: 0.7525 (m110) cc_final: 0.7014 (t0) REVERT: b 251 LYS cc_start: 0.4865 (tttt) cc_final: 0.4652 (tttt) REVERT: b 499 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: b 554 ASN cc_start: 0.7933 (t0) cc_final: 0.7403 (t0) REVERT: b 608 LYS cc_start: 0.7801 (mttm) cc_final: 0.7128 (mttt) REVERT: b 664 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8515 (m) outliers start: 47 outliers final: 40 residues processed: 176 average time/residue: 0.1247 time to fit residues: 34.9555 Evaluate side-chains 169 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 452 LYS Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 630 LEU Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain h residue 1090 THR Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 398 ASN Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 630 LEU Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain c residue 664 VAL Chi-restraints excluded: chain c residue 680 THR Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 398 ASN b 51 ASN b 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093692 restraints weight = 28405.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094163 restraints weight = 19663.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.094943 restraints weight = 14813.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095150 restraints weight = 12836.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095167 restraints weight = 11305.153| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18705 Z= 0.157 Angle : 0.507 9.527 25320 Z= 0.275 Chirality : 0.045 0.172 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.576 25.334 2520 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.53 % Allowed : 16.69 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.17), residues: 2277 helix: 0.34 (0.25), residues: 456 sheet: -0.27 (0.24), residues: 489 loop : -1.43 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 325 TYR 0.026 0.001 TYR b 511 PHE 0.017 0.001 PHE c 296 TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 Details of bonding type rmsd covalent geometry : bond 0.00369 (18702) covalent geometry : angle 0.50709 (25314) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.69619 ( 6) hydrogen bonds : bond 0.03262 ( 611) hydrogen bonds : angle 5.42741 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.86 seconds wall clock time: 40 minutes 17.98 seconds (2417.98 seconds total)