Starting phenix.real_space_refine on Mon Jun 16 04:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_14873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_14873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_14873.map" model { file = "/net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_14873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqp_14873/06_2025/7zqp_14873.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.31, per 1000 atoms: 0.56 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: 5.12 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.89 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: 7.56 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 0.00 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: 0.280 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.620 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.530 ------------------------------------------------------------------------------- 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 : 5.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (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 TRP 0.008 0.001 TRP d 369 HIS 0.003 0.001 HIS c 207 PHE 0.008 0.001 PHE b 538 TYR 0.023 0.001 TYR c 409 ARG 0.004 0.000 ARG d 224 Details of bonding type rmsd hydrogen bonds : bond 0.21883 ( 611) hydrogen bonds : angle 9.76463 ( 1758) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.43084 ( 6) covalent geometry : bond 0.00304 (18702) covalent geometry : angle 0.47989 (25314) *********************** 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 : 2.160 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: 0.7532 (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: 0.8118 (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: 0.8119 (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: 0.7783 (ttp) REVERT: c 413 ASP cc_start: 0.8201 (m-30) cc_final: 0.7934 (m-30) REVERT: c 508 TYR cc_start: 0.8028 (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: 0.7131 (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: 0.7226 (t0) REVERT: b 330 ARG cc_start: 0.6886 (mtt90) cc_final: 0.6539 (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: 0.7884 (p) REVERT: b 535 GLU cc_start: 0.7560 (mp0) cc_final: 0.7286 (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: 0.7872 (m-40) REVERT: b 641 TYR cc_start: 0.7647 (m-80) cc_final: 0.7390 (m-80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3038 time to fit residues: 109.2152 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 : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.089245 restraints weight = 28380.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.091071 restraints weight = 16696.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.092262 restraints weight = 11784.106| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18705 Z= 0.144 Angle : 0.526 10.262 25320 Z= 0.286 Chirality : 0.046 0.170 2757 Planarity : 0.004 0.046 3279 Dihedral : 4.429 25.144 2520 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.75 % Allowed : 6.31 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2277 helix: 0.57 (0.26), residues: 453 sheet: -0.48 (0.22), residues: 573 loop : -0.95 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 156 HIS 0.004 0.001 HIS c 207 PHE 0.012 0.001 PHE d 662 TYR 0.016 0.001 TYR c 172 ARG 0.004 0.000 ARG c 644 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 611) hydrogen bonds : angle 6.32644 ( 1758) SS BOND : bond 0.00391 ( 3) SS BOND : angle 0.65071 ( 6) covalent geometry : bond 0.00324 (18702) covalent geometry : angle 0.52563 (25314) *********************** 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 182 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6399 (ppp) cc_final: 0.5685 (ttp) REVERT: d 217 LYS cc_start: 0.7179 (mppt) cc_final: 0.6658 (ttmt) REVERT: d 251 LYS cc_start: 0.4671 (tttt) cc_final: 0.4438 (tttt) REVERT: d 436 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6260 (mt-10) REVERT: d 633 SER cc_start: 0.7810 (t) cc_final: 0.7413 (p) REVERT: d 646 TYR cc_start: 0.8288 (t80) cc_final: 0.7826 (t80) REVERT: h 1090 THR cc_start: 0.7772 (m) cc_final: 0.7224 (p) REVERT: h 1095 GLN cc_start: 0.8145 (tp40) cc_final: 0.7892 (tp40) REVERT: c 47 ASP cc_start: 0.8045 (m-30) cc_final: 0.7608 (p0) REVERT: c 338 MET cc_start: 0.8198 (ttp) cc_final: 0.7975 (ttp) REVERT: c 438 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: c 448 ASP cc_start: 0.7310 (p0) cc_final: 0.7045 (p0) REVERT: c 554 ASN cc_start: 0.8526 (t0) cc_final: 0.7827 (t0) REVERT: b 62 SER cc_start: 0.8639 (p) cc_final: 0.8427 (p) REVERT: b 143 ASN cc_start: 0.7654 (m110) cc_final: 0.7398 (t0) REVERT: b 217 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6934 (ttmt) REVERT: b 266 VAL cc_start: 0.8887 (t) cc_final: 0.8603 (p) REVERT: b 465 MET cc_start: 0.8140 (tpp) cc_final: 0.7897 (mmm) REVERT: b 566 TYR cc_start: 0.7790 (t80) cc_final: 0.7502 (t80) REVERT: b 608 LYS cc_start: 0.7628 (mttm) cc_final: 0.7288 (mttt) REVERT: b 623 ASP cc_start: 0.8218 (m-30) cc_final: 0.7982 (m-30) outliers start: 15 outliers final: 12 residues processed: 178 average time/residue: 0.2865 time to fit residues: 80.6020 Evaluate side-chains 158 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 177 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.108643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089119 restraints weight = 28968.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.089764 restraints weight = 19742.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.090508 restraints weight = 14392.159| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 18705 Z= 0.324 Angle : 0.676 13.104 25320 Z= 0.362 Chirality : 0.051 0.238 2757 Planarity : 0.005 0.044 3279 Dihedral : 5.289 26.070 2520 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.69 % Allowed : 10.28 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2277 helix: 0.02 (0.24), residues: 435 sheet: -0.62 (0.22), residues: 552 loop : -1.22 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 156 HIS 0.008 0.002 HIS c 207 PHE 0.020 0.002 PHE c 296 TYR 0.022 0.003 TYR b 416 ARG 0.011 0.001 ARG b 330 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 611) hydrogen bonds : angle 6.45428 ( 1758) SS BOND : bond 0.00909 ( 3) SS BOND : angle 1.14030 ( 6) covalent geometry : bond 0.00766 (18702) covalent geometry : angle 0.67549 (25314) *********************** 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 179 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: d 217 LYS cc_start: 0.7366 (mppt) cc_final: 0.6880 (ttmt) REVERT: d 256 ASP cc_start: 0.6833 (t0) cc_final: 0.6597 (t0) REVERT: d 448 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6792 (p0) REVERT: d 633 SER cc_start: 0.7846 (t) cc_final: 0.7550 (p) REVERT: j 1108 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7893 (mt-10) REVERT: h 1095 GLN cc_start: 0.8194 (tp40) cc_final: 0.7942 (tp40) REVERT: i 1102 MET cc_start: 0.7971 (mtt) cc_final: 0.7722 (mtt) REVERT: c 47 ASP cc_start: 0.8143 (m-30) cc_final: 0.7903 (p0) REVERT: c 306 ASP cc_start: 0.7950 (t0) cc_final: 0.7711 (t0) REVERT: c 438 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: c 448 ASP cc_start: 0.7406 (p0) cc_final: 0.7099 (p0) REVERT: c 605 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7302 (pp) REVERT: b 143 ASN cc_start: 0.7619 (m110) cc_final: 0.7186 (t0) REVERT: b 198 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: b 217 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7303 (ttmt) REVERT: b 251 LYS cc_start: 0.4675 (tttt) cc_final: 0.3666 (tttt) REVERT: b 465 MET cc_start: 0.8359 (tpp) cc_final: 0.8106 (mmm) REVERT: b 608 LYS cc_start: 0.7968 (mttm) cc_final: 0.7371 (mttt) REVERT: b 664 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8627 (m) outliers start: 34 outliers final: 24 residues processed: 177 average time/residue: 0.2820 time to fit residues: 79.1019 Evaluate side-chains 157 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 65 SER 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 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 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 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 497 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 81 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** c 591 ASN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.088904 restraints weight = 28965.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.090299 restraints weight = 17822.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090968 restraints weight = 12719.931| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2141 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= 0.178 Angle : 0.532 10.335 25320 Z= 0.289 Chirality : 0.046 0.225 2757 Planarity : 0.004 0.042 3279 Dihedral : 4.850 25.380 2520 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.74 % Allowed : 12.47 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2277 helix: 0.27 (0.25), residues: 435 sheet: -0.64 (0.22), residues: 576 loop : -1.22 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS c 107 PHE 0.016 0.002 PHE c 296 TYR 0.015 0.002 TYR d 511 ARG 0.006 0.000 ARG b 330 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 611) hydrogen bonds : angle 5.97133 ( 1758) SS BOND : bond 0.00520 ( 3) SS BOND : angle 0.88561 ( 6) covalent geometry : bond 0.00414 (18702) covalent geometry : angle 0.53181 (25314) *********************** 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 178 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6381 (ppp) cc_final: 0.6022 (ttp) REVERT: d 217 LYS cc_start: 0.7198 (mppt) cc_final: 0.6659 (ttmt) REVERT: d 448 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6734 (p0) REVERT: d 633 SER cc_start: 0.7765 (t) cc_final: 0.7457 (p) REVERT: h 1090 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7681 (p) REVERT: i 1102 MET cc_start: 0.7914 (mtt) cc_final: 0.7654 (mtt) REVERT: i 1108 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7213 (mt-10) REVERT: c 47 ASP cc_start: 0.8045 (m-30) cc_final: 0.7688 (p0) REVERT: c 306 ASP cc_start: 0.7744 (t0) cc_final: 0.7483 (t0) REVERT: c 438 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: c 448 ASP cc_start: 0.7477 (p0) cc_final: 0.7132 (p0) REVERT: c 554 ASN cc_start: 0.8544 (t0) cc_final: 0.7950 (t0) REVERT: c 579 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8319 (m-10) REVERT: c 605 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7376 (pp) REVERT: b 143 ASN cc_start: 0.7561 (m110) cc_final: 0.7101 (t0) REVERT: b 198 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: b 217 LYS cc_start: 0.7604 (ttpt) cc_final: 0.7219 (ttmt) REVERT: b 251 LYS cc_start: 0.4482 (tttt) cc_final: 0.3864 (tttt) REVERT: b 266 VAL cc_start: 0.8894 (t) cc_final: 0.8622 (p) REVERT: b 465 MET cc_start: 0.8336 (tpp) cc_final: 0.8052 (mmm) REVERT: b 608 LYS cc_start: 0.7932 (mttm) cc_final: 0.7285 (mttt) REVERT: b 623 ASP cc_start: 0.8333 (m-30) cc_final: 0.7946 (m-30) REVERT: b 632 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7384 (mp) REVERT: b 664 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8649 (m) outliers start: 35 outliers final: 22 residues processed: 173 average time/residue: 0.2977 time to fit residues: 82.0898 Evaluate side-chains 163 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 65 SER 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 448 ASP Chi-restraints excluded: chain d residue 562 THR 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 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 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL 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 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 184 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** b 68 GLN b 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.088847 restraints weight = 29138.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089355 restraints weight = 18353.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.089784 restraints weight = 15580.503| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 18705 Z= 0.290 Angle : 0.635 12.005 25320 Z= 0.341 Chirality : 0.049 0.220 2757 Planarity : 0.004 0.041 3279 Dihedral : 5.297 26.472 2520 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.98 % Allowed : 13.56 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2277 helix: -0.11 (0.24), residues: 435 sheet: -0.80 (0.22), residues: 570 loop : -1.41 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP d 156 HIS 0.006 0.002 HIS c 207 PHE 0.021 0.002 PHE c 296 TYR 0.020 0.002 TYR b 416 ARG 0.004 0.001 ARG d 179 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 611) hydrogen bonds : angle 6.15625 ( 1758) SS BOND : bond 0.00722 ( 3) SS BOND : angle 0.97346 ( 6) covalent geometry : bond 0.00686 (18702) covalent geometry : angle 0.63492 (25314) *********************** 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 200 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 2.406 Fit side-chains REVERT: d 1 MET cc_start: 0.6422 (ppp) cc_final: 0.6068 (ttp) REVERT: d 217 LYS cc_start: 0.7092 (mppt) cc_final: 0.6590 (ttmt) REVERT: d 298 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: d 633 SER cc_start: 0.7848 (t) cc_final: 0.7540 (p) REVERT: j 1090 THR cc_start: 0.7775 (m) cc_final: 0.7194 (p) REVERT: i 1102 MET cc_start: 0.8023 (mtt) cc_final: 0.7779 (mtt) REVERT: i 1108 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7278 (mt-10) REVERT: c 47 ASP cc_start: 0.8173 (m-30) cc_final: 0.7912 (p0) REVERT: c 306 ASP cc_start: 0.7944 (t0) cc_final: 0.7555 (t0) REVERT: c 438 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: c 480 ASP cc_start: 0.7160 (p0) cc_final: 0.6952 (p0) REVERT: c 554 ASN cc_start: 0.8595 (t0) cc_final: 0.8034 (t0) REVERT: c 579 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: c 605 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7454 (pp) REVERT: b 143 ASN cc_start: 0.7640 (m110) cc_final: 0.7026 (t0) REVERT: b 198 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: b 266 VAL cc_start: 0.8904 (t) cc_final: 0.8649 (p) REVERT: b 465 MET cc_start: 0.8339 (tpp) cc_final: 0.8109 (mmm) REVERT: b 499 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: b 554 ASN cc_start: 0.8419 (t0) cc_final: 0.8174 (t0) REVERT: b 608 LYS cc_start: 0.7901 (mttm) cc_final: 0.7273 (mttt) REVERT: b 632 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7452 (mp) REVERT: b 664 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8619 (m) outliers start: 60 outliers final: 43 residues processed: 194 average time/residue: 0.2832 time to fit residues: 88.1194 Evaluate side-chains 185 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 65 SER 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 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 298 GLU Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 442 VAL 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 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 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 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 266 VAL 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 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 168 VAL Chi-restraints excluded: chain b residue 198 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 177 optimal weight: 0.1980 chunk 204 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 51 ASN d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 68 GLN b 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.091102 restraints weight = 28856.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.091797 restraints weight = 19426.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.092359 restraints weight = 14231.892| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18705 Z= 0.225 Angle : 0.568 10.500 25320 Z= 0.307 Chirality : 0.047 0.195 2757 Planarity : 0.004 0.040 3279 Dihedral : 5.078 26.048 2520 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.88 % Allowed : 14.61 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2277 helix: -0.00 (0.24), residues: 435 sheet: -0.77 (0.22), residues: 546 loop : -1.47 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 PHE 0.019 0.002 PHE c 296 TYR 0.017 0.002 TYR c 511 ARG 0.003 0.000 ARG c 560 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 611) hydrogen bonds : angle 5.91721 ( 1758) SS BOND : bond 0.00600 ( 3) SS BOND : angle 0.87630 ( 6) covalent geometry : bond 0.00530 (18702) covalent geometry : angle 0.56753 (25314) *********************** 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 195 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6401 (ppp) cc_final: 0.6040 (ttp) REVERT: d 217 LYS cc_start: 0.7043 (mppt) cc_final: 0.6563 (ttmt) REVERT: d 298 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: d 633 SER cc_start: 0.7817 (t) cc_final: 0.7513 (p) REVERT: j 1090 THR cc_start: 0.7749 (m) cc_final: 0.7174 (p) REVERT: h 1090 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7682 (p) REVERT: i 1102 MET cc_start: 0.7957 (mtt) cc_final: 0.7702 (mtt) REVERT: i 1108 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7207 (mt-10) REVERT: c 47 ASP cc_start: 0.8050 (m-30) cc_final: 0.7674 (p0) REVERT: c 306 ASP cc_start: 0.7831 (t0) cc_final: 0.7518 (t0) REVERT: c 579 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8283 (m-10) REVERT: c 611 SER cc_start: 0.7583 (m) cc_final: 0.7251 (t) REVERT: b 143 ASN cc_start: 0.7634 (m110) cc_final: 0.6987 (t0) REVERT: b 198 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: b 217 LYS cc_start: 0.7404 (ttpt) cc_final: 0.7009 (ttmt) REVERT: b 266 VAL cc_start: 0.8908 (t) cc_final: 0.8636 (p) REVERT: b 465 MET cc_start: 0.8360 (tpp) cc_final: 0.8121 (mmm) REVERT: b 499 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: b 554 ASN cc_start: 0.8371 (t0) cc_final: 0.8085 (t0) REVERT: b 608 LYS cc_start: 0.7900 (mttm) cc_final: 0.7238 (mttt) REVERT: b 632 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7426 (mp) REVERT: b 664 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8661 (m) outliers start: 58 outliers final: 43 residues processed: 188 average time/residue: 0.2749 time to fit residues: 82.9148 Evaluate side-chains 183 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 65 SER 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 298 GLU 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 494 LEU 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 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 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL 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 600 LEU 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 146 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 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 222 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 51 ASN d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 360 ASN b 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.095822 restraints weight = 27852.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097655 restraints weight = 16455.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098646 restraints weight = 11734.459| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18705 Z= 0.112 Angle : 0.474 7.825 25320 Z= 0.258 Chirality : 0.044 0.166 2757 Planarity : 0.003 0.039 3279 Dihedral : 4.530 25.044 2520 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.89 % Allowed : 15.95 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2277 helix: 0.37 (0.25), residues: 438 sheet: -0.62 (0.22), residues: 552 loop : -1.31 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 369 HIS 0.002 0.001 HIS b 372 PHE 0.016 0.001 PHE c 296 TYR 0.014 0.001 TYR d 646 ARG 0.003 0.000 ARG c 644 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 611) hydrogen bonds : angle 5.50609 ( 1758) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.66717 ( 6) covalent geometry : bond 0.00255 (18702) covalent geometry : angle 0.47400 (25314) *********************** 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 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 2.601 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6470 (ppp) cc_final: 0.6180 (ttp) REVERT: d 217 LYS cc_start: 0.7048 (mppt) cc_final: 0.6563 (ttmt) REVERT: d 633 SER cc_start: 0.7858 (t) cc_final: 0.7554 (p) REVERT: j 1090 THR cc_start: 0.7490 (m) cc_final: 0.7037 (p) REVERT: h 1090 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7562 (p) REVERT: i 1095 GLN cc_start: 0.7808 (tp40) cc_final: 0.7528 (tp-100) REVERT: i 1102 MET cc_start: 0.7836 (mtt) cc_final: 0.7588 (mtt) REVERT: i 1108 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7324 (mt-10) REVERT: c 18 LEU cc_start: 0.8305 (mt) cc_final: 0.8103 (mt) REVERT: c 47 ASP cc_start: 0.8061 (m-30) cc_final: 0.7676 (p0) REVERT: c 306 ASP cc_start: 0.7343 (t0) cc_final: 0.6951 (t0) REVERT: c 465 MET cc_start: 0.8426 (tpp) cc_final: 0.8095 (mmm) REVERT: c 554 ASN cc_start: 0.8507 (t0) cc_final: 0.7911 (t0) REVERT: c 579 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: c 611 SER cc_start: 0.7476 (m) cc_final: 0.7138 (t) REVERT: b 143 ASN cc_start: 0.7556 (m110) cc_final: 0.7039 (t0) REVERT: b 217 LYS cc_start: 0.7318 (ttpt) cc_final: 0.6931 (ttmt) REVERT: b 251 LYS cc_start: 0.4595 (tttt) cc_final: 0.4331 (tttt) REVERT: b 266 VAL cc_start: 0.8896 (t) cc_final: 0.8589 (p) REVERT: b 554 ASN cc_start: 0.8086 (t0) cc_final: 0.7633 (t0) REVERT: b 608 LYS cc_start: 0.7807 (mttm) cc_final: 0.7139 (mttt) REVERT: b 664 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8562 (m) outliers start: 38 outliers final: 28 residues processed: 191 average time/residue: 0.2955 time to fit residues: 90.2369 Evaluate side-chains 170 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 65 SER 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 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 497 ILE 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 184 VAL Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 337 THR 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 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 437 VAL Chi-restraints excluded: chain b residue 451 ILE 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 25 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 51 ASN d 569 ASN d 591 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3275 r_free = 0.3275 target = 0.111542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.091972 restraints weight = 28542.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.092221 restraints weight = 19123.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092623 restraints weight = 16434.255| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18705 Z= 0.216 Angle : 0.566 9.777 25320 Z= 0.305 Chirality : 0.047 0.196 2757 Planarity : 0.004 0.039 3279 Dihedral : 4.919 25.910 2520 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.43 % Allowed : 16.05 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2277 helix: 0.23 (0.25), residues: 435 sheet: -0.73 (0.22), residues: 564 loop : -1.40 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 156 HIS 0.004 0.001 HIS d 107 PHE 0.019 0.002 PHE c 296 TYR 0.016 0.002 TYR b 511 ARG 0.003 0.000 ARG b 325 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 611) hydrogen bonds : angle 5.77083 ( 1758) SS BOND : bond 0.00544 ( 3) SS BOND : angle 1.20400 ( 6) covalent geometry : bond 0.00509 (18702) covalent geometry : angle 0.56580 (25314) *********************** 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 192 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 2.125 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6327 (ppp) cc_final: 0.5963 (ttp) REVERT: d 28 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8105 (mp) REVERT: d 149 ILE cc_start: 0.7903 (mm) cc_final: 0.7560 (mt) REVERT: d 217 LYS cc_start: 0.6979 (mppt) cc_final: 0.6530 (ttmt) REVERT: d 298 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: d 633 SER cc_start: 0.7830 (t) cc_final: 0.7504 (p) REVERT: j 1090 THR cc_start: 0.7747 (m) cc_final: 0.7192 (p) REVERT: h 1090 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7685 (p) REVERT: i 1095 GLN cc_start: 0.7757 (tp40) cc_final: 0.7471 (tp-100) REVERT: i 1102 MET cc_start: 0.7947 (mtt) cc_final: 0.7700 (mtt) REVERT: i 1108 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7207 (mt-10) REVERT: c 47 ASP cc_start: 0.8045 (m-30) cc_final: 0.7684 (p0) REVERT: c 306 ASP cc_start: 0.7506 (t0) cc_final: 0.7076 (t0) REVERT: c 554 ASN cc_start: 0.8514 (t0) cc_final: 0.7955 (t0) REVERT: c 579 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8304 (m-10) REVERT: c 611 SER cc_start: 0.7607 (m) cc_final: 0.7269 (t) REVERT: b 143 ASN cc_start: 0.7589 (m110) cc_final: 0.7026 (t0) REVERT: b 217 LYS cc_start: 0.7396 (ttpt) cc_final: 0.7002 (ttmt) REVERT: b 266 VAL cc_start: 0.8913 (t) cc_final: 0.8623 (p) REVERT: b 554 ASN cc_start: 0.8101 (t0) cc_final: 0.7710 (t0) REVERT: b 608 LYS cc_start: 0.7864 (mttm) cc_final: 0.7211 (mttt) REVERT: b 632 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7480 (mp) REVERT: b 664 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8625 (m) outliers start: 49 outliers final: 40 residues processed: 183 average time/residue: 0.2894 time to fit residues: 84.9119 Evaluate side-chains 186 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 65 SER 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 298 GLU 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 452 LYS 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 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 184 VAL 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 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 437 VAL Chi-restraints excluded: chain b residue 451 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 51 ASN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3299 r_free = 0.3299 target = 0.113215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.092352 restraints weight = 28526.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094179 restraints weight = 16808.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095342 restraints weight = 11834.625| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2644 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= 0.119 Angle : 0.487 7.661 25320 Z= 0.264 Chirality : 0.045 0.166 2757 Planarity : 0.003 0.039 3279 Dihedral : 4.492 25.043 2520 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.53 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2277 helix: 0.27 (0.25), residues: 456 sheet: -0.28 (0.24), residues: 486 loop : -1.43 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 369 HIS 0.005 0.001 HIS b 339 PHE 0.016 0.001 PHE c 296 TYR 0.017 0.001 TYR d 646 ARG 0.004 0.000 ARG b 408 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 611) hydrogen bonds : angle 5.42753 ( 1758) SS BOND : bond 0.00467 ( 3) SS BOND : angle 0.89083 ( 6) covalent geometry : bond 0.00272 (18702) covalent geometry : angle 0.48733 (25314) *********************** 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 193 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6320 (ppp) cc_final: 0.6035 (ttp) REVERT: d 149 ILE cc_start: 0.7894 (mm) cc_final: 0.7542 (mt) REVERT: d 217 LYS cc_start: 0.7018 (mppt) cc_final: 0.6553 (ttmt) REVERT: d 298 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: d 560 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7486 (mtp-110) REVERT: d 633 SER cc_start: 0.7763 (t) cc_final: 0.7450 (p) REVERT: j 1090 THR cc_start: 0.7572 (m) cc_final: 0.7100 (p) REVERT: h 1090 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7480 (p) REVERT: i 1095 GLN cc_start: 0.7781 (tp40) cc_final: 0.7519 (tp-100) REVERT: i 1102 MET cc_start: 0.7865 (mtt) cc_final: 0.7628 (mtt) REVERT: i 1108 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7145 (mt-10) REVERT: c 47 ASP cc_start: 0.8055 (m-30) cc_final: 0.7674 (p0) REVERT: c 306 ASP cc_start: 0.7429 (t0) cc_final: 0.7028 (t0) REVERT: c 406 ASP cc_start: 0.7105 (t0) cc_final: 0.6809 (t70) REVERT: c 465 MET cc_start: 0.8403 (tpp) cc_final: 0.8075 (mmm) REVERT: c 554 ASN cc_start: 0.8488 (t0) cc_final: 0.7908 (t0) REVERT: c 579 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: c 611 SER cc_start: 0.7515 (m) cc_final: 0.7151 (t) REVERT: b 143 ASN cc_start: 0.7530 (m110) cc_final: 0.7002 (t0) REVERT: b 198 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: b 217 LYS cc_start: 0.7342 (ttpt) cc_final: 0.6949 (ttmt) REVERT: b 251 LYS cc_start: 0.4674 (tttt) cc_final: 0.3872 (tttt) REVERT: b 336 ASP cc_start: 0.6551 (m-30) cc_final: 0.6125 (m-30) REVERT: b 499 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: b 554 ASN cc_start: 0.7940 (t0) cc_final: 0.7440 (t0) REVERT: b 608 LYS cc_start: 0.7793 (mttm) cc_final: 0.7128 (mttt) REVERT: b 664 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8546 (m) outliers start: 51 outliers final: 38 residues processed: 186 average time/residue: 0.2753 time to fit residues: 81.9290 Evaluate side-chains 177 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 65 SER 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 298 GLU Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 442 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 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 333 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 382 VAL 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 198 GLU Chi-restraints excluded: chain b residue 382 VAL 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 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091207 restraints weight = 28632.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.092988 restraints weight = 16892.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094144 restraints weight = 11971.447| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18705 Z= 0.155 Angle : 0.512 8.181 25320 Z= 0.276 Chirality : 0.045 0.174 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.608 25.136 2520 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2277 helix: 0.46 (0.25), residues: 438 sheet: -0.27 (0.24), residues: 486 loop : -1.42 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 PHE 0.017 0.001 PHE c 296 TYR 0.021 0.001 TYR b 640 ARG 0.003 0.000 ARG b 325 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 611) hydrogen bonds : angle 5.48561 ( 1758) SS BOND : bond 0.00467 ( 3) SS BOND : angle 0.82402 ( 6) covalent geometry : bond 0.00363 (18702) covalent geometry : angle 0.51151 (25314) ********************** 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 192 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 2.099 Fit side-chains revert: symmetry clash REVERT: d 1 MET cc_start: 0.6417 (ppp) cc_final: 0.6166 (ttp) REVERT: d 149 ILE cc_start: 0.7921 (mm) cc_final: 0.7568 (mt) REVERT: d 217 LYS cc_start: 0.6769 (mppt) cc_final: 0.6370 (ttmt) REVERT: d 298 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: d 633 SER cc_start: 0.7832 (t) cc_final: 0.7508 (p) REVERT: j 1090 THR cc_start: 0.7602 (m) cc_final: 0.7139 (p) REVERT: h 1090 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7521 (p) REVERT: i 1095 GLN cc_start: 0.7791 (tp40) cc_final: 0.7532 (tp-100) REVERT: i 1102 MET cc_start: 0.7879 (mtt) cc_final: 0.7611 (mtt) REVERT: i 1108 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7197 (mt-10) REVERT: i 1120 ASN cc_start: 0.7867 (p0) cc_final: 0.7353 (p0) REVERT: c 47 ASP cc_start: 0.8061 (m-30) cc_final: 0.7679 (p0) REVERT: c 306 ASP cc_start: 0.7454 (t0) cc_final: 0.6955 (t0) REVERT: c 406 ASP cc_start: 0.7148 (t0) cc_final: 0.6813 (t70) REVERT: c 465 MET cc_start: 0.8400 (tpp) cc_final: 0.8055 (mmm) REVERT: c 554 ASN cc_start: 0.8510 (t0) cc_final: 0.7935 (t0) REVERT: c 579 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8239 (m-10) REVERT: c 611 SER cc_start: 0.7549 (m) cc_final: 0.7189 (t) REVERT: b 143 ASN cc_start: 0.7546 (m110) cc_final: 0.7043 (t0) REVERT: b 198 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: b 217 LYS cc_start: 0.7358 (ttpt) cc_final: 0.6969 (ttmt) REVERT: b 251 LYS cc_start: 0.4599 (tttt) cc_final: 0.4034 (tttt) REVERT: b 266 VAL cc_start: 0.8808 (t) cc_final: 0.8555 (p) REVERT: b 336 ASP cc_start: 0.6560 (m-30) cc_final: 0.6162 (m-30) REVERT: b 499 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: b 554 ASN cc_start: 0.8050 (t0) cc_final: 0.7579 (t0) REVERT: b 608 LYS cc_start: 0.7803 (mttm) cc_final: 0.7151 (mttt) REVERT: b 664 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8532 (m) REVERT: b 675 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7507 (m-30) outliers start: 49 outliers final: 40 residues processed: 183 average time/residue: 0.2785 time to fit residues: 81.9536 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 : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 65 SER 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 298 GLU Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 442 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 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 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 198 GLU Chi-restraints excluded: chain b residue 382 VAL 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 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 49 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** b 51 ASN b 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092258 restraints weight = 28625.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092934 restraints weight = 17868.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094048 restraints weight = 14974.129| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18705 Z= 0.176 Angle : 0.536 9.967 25320 Z= 0.289 Chirality : 0.046 0.181 2757 Planarity : 0.003 0.037 3279 Dihedral : 4.721 25.559 2520 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.58 % Allowed : 16.49 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2277 helix: 0.22 (0.25), residues: 456 sheet: -0.36 (0.23), residues: 498 loop : -1.48 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 369 HIS 0.004 0.001 HIS d 107 PHE 0.018 0.002 PHE c 296 TYR 0.023 0.002 TYR b 640 ARG 0.004 0.000 ARG b 325 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 611) hydrogen bonds : angle 5.56001 ( 1758) SS BOND : bond 0.00527 ( 3) SS BOND : angle 0.87481 ( 6) covalent geometry : bond 0.00415 (18702) covalent geometry : angle 0.53627 (25314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4828.72 seconds wall clock time: 85 minutes 23.63 seconds (5123.63 seconds total)