Starting phenix.real_space_refine on Wed Apr 10 03:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_14873.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_14873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_14873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_14873.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqp_14873/04_2024/7zqp_14873.pdb" } 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 Residue "d TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 1093": "OE1" <-> "OE2" Residue "c GLU 425": "OE1" <-> "OE2" Residue "c ASP 581": "OD1" <-> "OD2" Residue "c TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 695": "OE1" <-> "OE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 306": "OD1" <-> "OD2" Residue "b GLU 425": "OE1" <-> "OE2" Residue "b TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 499": "OE1" <-> "OE2" Residue "b PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.57, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 3.5 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: 2.58 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: 7.86 Time building geometry restraints manager: 7.35 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: 100.34 - 107.09: 381 107.09 - 113.85: 10294 113.85 - 120.61: 7439 120.61 - 127.37: 7054 127.37 - 134.13: 146 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 2.440 nonbonded pdb=" O LEU c 555 " pdb=" OG SER c 556 " model vdw 2.078 2.440 nonbonded pdb=" OD1 ASP c 302 " pdb=" NZ LYS c 441 " model vdw 2.079 2.520 nonbonded pdb=" OH TYR b 308 " pdb=" OE2 GLU b 436 " model vdw 2.085 2.440 nonbonded pdb=" O LYS b 230 " pdb=" NH1 ARG b 238 " model vdw 2.115 2.520 ... (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 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.990 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 50.320 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.090 ------------------------------------------------------------------------------- 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 18702 Z= 0.197 Angle : 0.480 4.698 25314 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.969 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: 0.3050 time to fit residues: 109.2798 Evaluate side-chains 152 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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: 10.0000 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 353 HIS d 569 ASN d 591 ASN d 622 GLN c 51 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 ASN b 506 GLN b 528 ASN ** b 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18702 Z= 0.345 Angle : 0.586 12.310 25314 Z= 0.315 Chirality : 0.048 0.214 2757 Planarity : 0.004 0.046 3279 Dihedral : 4.823 24.732 2520 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.94 % Allowed : 7.55 % Favored : 91.51 % 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: -1.02 (0.17), residues: 2277 helix: 0.48 (0.26), residues: 435 sheet: -0.60 (0.21), residues: 600 loop : -1.12 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 156 HIS 0.007 0.002 HIS c 207 PHE 0.015 0.002 PHE c 296 TYR 0.019 0.002 TYR b 416 ARG 0.004 0.001 ARG b 420 *********************** 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 175 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.992 Fit side-chains REVERT: d 217 LYS cc_start: 0.7234 (mppt) cc_final: 0.6573 (ttmt) REVERT: d 252 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6717 (mm-30) REVERT: d 281 ASP cc_start: 0.8003 (t0) cc_final: 0.7712 (t70) REVERT: d 624 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7658 (mtmm) REVERT: d 633 SER cc_start: 0.8050 (t) cc_final: 0.7662 (p) REVERT: h 1090 THR cc_start: 0.8173 (m) cc_final: 0.7712 (p) REVERT: h 1095 GLN cc_start: 0.8228 (tp40) cc_final: 0.7989 (tp40) REVERT: i 1108 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7230 (mt-10) REVERT: i 1110 SER cc_start: 0.8786 (m) cc_final: 0.8507 (t) REVERT: c 1 MET cc_start: 0.6551 (ppp) cc_final: 0.5596 (ttt) REVERT: c 338 MET cc_start: 0.8174 (ttp) cc_final: 0.7933 (ttp) REVERT: c 438 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: c 554 ASN cc_start: 0.8512 (t0) cc_final: 0.7770 (t0) REVERT: b 143 ASN cc_start: 0.7623 (m110) cc_final: 0.7181 (t0) REVERT: b 217 LYS cc_start: 0.7355 (ttpt) cc_final: 0.6936 (ttmt) REVERT: b 465 MET cc_start: 0.8141 (tpp) cc_final: 0.7911 (mmm) REVERT: b 566 TYR cc_start: 0.7925 (t80) cc_final: 0.7659 (t80) REVERT: b 608 LYS cc_start: 0.7912 (mttm) cc_final: 0.7152 (mttt) REVERT: b 664 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8591 (m) outliers start: 19 outliers final: 15 residues processed: 170 average time/residue: 0.2881 time to fit residues: 77.1629 Evaluate side-chains 153 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 437 VAL 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 448 ASP Chi-restraints excluded: chain c residue 661 SER Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 664 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN i1095 GLN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 528 ASN b 636 ASN b 709 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18702 Z= 0.300 Angle : 0.541 10.764 25314 Z= 0.292 Chirality : 0.047 0.217 2757 Planarity : 0.004 0.045 3279 Dihedral : 4.809 24.065 2520 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.74 % Allowed : 10.93 % Favored : 87.33 % 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: -1.02 (0.17), residues: 2277 helix: 0.56 (0.26), residues: 417 sheet: -0.56 (0.22), residues: 582 loop : -1.15 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 156 HIS 0.005 0.001 HIS c 207 PHE 0.014 0.002 PHE c 296 TYR 0.016 0.002 TYR b 416 ARG 0.004 0.000 ARG c 644 *********************** 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 fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 2.220 Fit side-chains REVERT: d 217 LYS cc_start: 0.6827 (mppt) cc_final: 0.6389 (ttmt) REVERT: d 256 ASP cc_start: 0.6771 (t0) cc_final: 0.6247 (t0) REVERT: d 281 ASP cc_start: 0.8125 (t0) cc_final: 0.7798 (t70) REVERT: d 306 ASP cc_start: 0.7956 (t70) cc_final: 0.7725 (t0) REVERT: d 612 ILE cc_start: 0.8168 (mt) cc_final: 0.7900 (mt) REVERT: d 633 SER cc_start: 0.7885 (t) cc_final: 0.7514 (p) REVERT: h 1090 THR cc_start: 0.8150 (m) cc_final: 0.7691 (p) REVERT: h 1095 GLN cc_start: 0.8232 (tp40) cc_final: 0.8011 (tp40) REVERT: i 1110 SER cc_start: 0.8742 (m) cc_final: 0.8499 (t) REVERT: c 338 MET cc_start: 0.8229 (ttp) cc_final: 0.8002 (ttp) REVERT: c 521 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7269 (p0) REVERT: c 605 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7018 (pp) REVERT: b 143 ASN cc_start: 0.7598 (m110) cc_final: 0.7056 (t0) REVERT: b 198 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: b 217 LYS cc_start: 0.7396 (ttpt) cc_final: 0.6957 (ttmt) REVERT: b 465 MET cc_start: 0.8176 (tpp) cc_final: 0.7931 (mmm) REVERT: b 608 LYS cc_start: 0.7973 (mttm) cc_final: 0.7240 (mttt) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.2864 time to fit residues: 79.5180 Evaluate side-chains 159 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 318 ASP Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 437 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 47 ASP Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 521 ASN 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 47 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 0.0050 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- 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 438 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 528 ASN b 68 GLN b 228 GLN b 528 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18702 Z= 0.354 Angle : 0.572 11.606 25314 Z= 0.307 Chirality : 0.047 0.234 2757 Planarity : 0.004 0.043 3279 Dihedral : 5.008 25.399 2520 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.93 % Allowed : 12.27 % Favored : 84.80 % 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: -1.18 (0.17), residues: 2277 helix: 0.36 (0.25), residues: 417 sheet: -0.56 (0.22), residues: 579 loop : -1.28 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 156 HIS 0.005 0.001 HIS d 107 PHE 0.018 0.002 PHE c 296 TYR 0.017 0.002 TYR b 416 ARG 0.003 0.001 ARG b 196 *********************** 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 196 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 2.066 Fit side-chains REVERT: d 217 LYS cc_start: 0.6851 (mppt) cc_final: 0.6523 (ttmt) REVERT: d 281 ASP cc_start: 0.8181 (t0) cc_final: 0.7925 (t70) REVERT: d 306 ASP cc_start: 0.7857 (t70) cc_final: 0.7635 (t0) REVERT: d 612 ILE cc_start: 0.8130 (mt) cc_final: 0.7867 (mt) REVERT: d 633 SER cc_start: 0.7949 (t) cc_final: 0.7593 (p) REVERT: h 1090 THR cc_start: 0.8184 (m) cc_final: 0.7749 (p) REVERT: i 1110 SER cc_start: 0.8800 (m) cc_final: 0.8542 (t) REVERT: c 338 MET cc_start: 0.8137 (ttp) cc_final: 0.7869 (ttp) REVERT: c 438 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: c 521 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7366 (p0) REVERT: c 579 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: c 605 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7232 (pp) REVERT: c 611 SER cc_start: 0.7466 (m) cc_final: 0.7119 (t) REVERT: b 51 ASN cc_start: 0.7774 (m110) cc_final: 0.7518 (m110) REVERT: b 143 ASN cc_start: 0.7639 (m110) cc_final: 0.6988 (t0) REVERT: b 198 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: b 217 LYS cc_start: 0.7350 (ttpt) cc_final: 0.6954 (ttmt) REVERT: b 465 MET cc_start: 0.8231 (tpp) cc_final: 0.7969 (mmm) REVERT: b 499 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: b 608 LYS cc_start: 0.7939 (mttm) cc_final: 0.7197 (mttt) REVERT: b 632 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7445 (mp) REVERT: b 664 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8597 (m) outliers start: 59 outliers final: 44 residues processed: 189 average time/residue: 0.2763 time to fit residues: 83.4634 Evaluate side-chains 179 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 127 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 318 ASP Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 437 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 450 THR Chi-restraints excluded: chain d residue 494 LEU Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 47 ASP Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 521 ASN 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 47 ASP 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 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 515 ASN 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 183 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 528 ASN c 591 ASN b 68 GLN b 228 GLN b 528 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18702 Z= 0.254 Angle : 0.507 9.583 25314 Z= 0.275 Chirality : 0.046 0.228 2757 Planarity : 0.003 0.042 3279 Dihedral : 4.751 24.446 2520 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.58 % Allowed : 14.26 % Favored : 83.16 % 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: -1.14 (0.17), residues: 2277 helix: 0.56 (0.26), residues: 417 sheet: -0.67 (0.21), residues: 618 loop : -1.25 (0.16), residues: 1242 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 0.016 0.002 PHE c 296 TYR 0.013 0.001 TYR j1088 ARG 0.002 0.000 ARG c 644 *********************** 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 191 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.112 Fit side-chains REVERT: d 217 LYS cc_start: 0.6775 (mppt) cc_final: 0.6413 (ttmt) REVERT: d 281 ASP cc_start: 0.8121 (t0) cc_final: 0.7806 (t70) REVERT: d 306 ASP cc_start: 0.7944 (t70) cc_final: 0.7613 (t0) REVERT: d 633 SER cc_start: 0.8010 (t) cc_final: 0.7645 (p) REVERT: h 1090 THR cc_start: 0.8132 (m) cc_final: 0.7684 (p) REVERT: i 1102 MET cc_start: 0.7853 (mtt) cc_final: 0.7585 (mtt) REVERT: i 1110 SER cc_start: 0.8733 (m) cc_final: 0.8492 (t) REVERT: c 338 MET cc_start: 0.8090 (ttp) cc_final: 0.7833 (ttp) REVERT: c 438 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: c 521 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7244 (p0) REVERT: c 554 ASN cc_start: 0.8561 (t0) cc_final: 0.7877 (t0) REVERT: c 579 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: c 605 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7244 (pp) REVERT: b 143 ASN cc_start: 0.7621 (m110) cc_final: 0.6996 (t0) REVERT: b 198 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: b 217 LYS cc_start: 0.7341 (ttpt) cc_final: 0.6938 (ttmt) REVERT: b 465 MET cc_start: 0.8155 (tpp) cc_final: 0.7921 (mmm) REVERT: b 608 LYS cc_start: 0.7929 (mttm) cc_final: 0.7174 (mttt) REVERT: b 632 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7451 (mp) REVERT: b 664 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8560 (m) outliers start: 52 outliers final: 37 residues processed: 185 average time/residue: 0.2854 time to fit residues: 85.6540 Evaluate side-chains 173 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 437 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 637 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 47 ASP Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 389 LYS Chi-restraints excluded: chain c residue 438 GLN Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 521 ASN 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 680 THR Chi-restraints excluded: chain b residue 47 ASP 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 515 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 c 438 GLN c 591 ASN b 51 ASN b 228 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18702 Z= 0.114 Angle : 0.429 5.757 25314 Z= 0.233 Chirality : 0.043 0.180 2757 Planarity : 0.003 0.040 3279 Dihedral : 4.016 22.985 2520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.84 % Allowed : 15.50 % Favored : 82.66 % 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: -0.80 (0.17), residues: 2277 helix: 0.94 (0.27), residues: 423 sheet: -0.45 (0.22), residues: 585 loop : -1.08 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 369 HIS 0.002 0.000 HIS c 372 PHE 0.012 0.001 PHE c 296 TYR 0.016 0.001 TYR j1088 ARG 0.003 0.000 ARG j1113 *********************** 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 212 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 2.238 Fit side-chains REVERT: d 217 LYS cc_start: 0.6938 (mppt) cc_final: 0.6250 (ttmt) REVERT: d 281 ASP cc_start: 0.7867 (t0) cc_final: 0.7626 (t70) REVERT: d 306 ASP cc_start: 0.7800 (t70) cc_final: 0.7484 (t70) REVERT: d 436 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6228 (mt-10) REVERT: d 443 LYS cc_start: 0.8122 (mttp) cc_final: 0.7684 (mtmm) REVERT: d 546 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6893 (mm-30) REVERT: d 633 SER cc_start: 0.8021 (t) cc_final: 0.7631 (p) REVERT: h 1087 GLN cc_start: 0.7115 (tt0) cc_final: 0.6754 (tt0) REVERT: h 1088 TYR cc_start: 0.5663 (p90) cc_final: 0.5433 (p90) REVERT: i 1095 GLN cc_start: 0.7835 (tp40) cc_final: 0.7523 (tp-100) REVERT: i 1110 SER cc_start: 0.8703 (m) cc_final: 0.8490 (t) REVERT: c 1 MET cc_start: 0.6482 (ppp) cc_final: 0.6225 (ttp) REVERT: c 18 LEU cc_start: 0.8320 (mt) cc_final: 0.8112 (mt) REVERT: c 47 ASP cc_start: 0.8415 (m-30) cc_final: 0.7995 (p0) REVERT: c 338 MET cc_start: 0.8046 (ttp) cc_final: 0.7734 (ttp) REVERT: c 465 MET cc_start: 0.8393 (tpp) cc_final: 0.8060 (mmm) REVERT: c 554 ASN cc_start: 0.8426 (t0) cc_final: 0.7729 (t0) REVERT: c 579 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8040 (m-10) REVERT: c 611 SER cc_start: 0.7247 (m) cc_final: 0.6870 (t) REVERT: b 143 ASN cc_start: 0.7563 (m110) cc_final: 0.6980 (t0) REVERT: b 217 LYS cc_start: 0.6997 (ttpt) cc_final: 0.6547 (tttt) REVERT: b 251 LYS cc_start: 0.4583 (tttt) cc_final: 0.4277 (tttt) REVERT: b 436 GLU cc_start: 0.6349 (mt-10) cc_final: 0.6057 (mt-10) REVERT: b 554 ASN cc_start: 0.8274 (t0) cc_final: 0.7780 (t0) REVERT: b 608 LYS cc_start: 0.7739 (mttm) cc_final: 0.7042 (mttt) REVERT: b 664 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8448 (m) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.2971 time to fit residues: 94.6222 Evaluate side-chains 171 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain 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 437 VAL Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 591 ASN 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 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 515 ASN Chi-restraints excluded: chain b residue 578 THR 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 212 optimal weight: 0.1980 chunk 24 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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 398 ASN c 528 ASN b 51 ASN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 228 GLN b 400 ASN b 528 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18702 Z= 0.356 Angle : 0.574 10.837 25314 Z= 0.306 Chirality : 0.047 0.221 2757 Planarity : 0.004 0.047 3279 Dihedral : 4.799 25.040 2520 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.88 % Allowed : 15.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2277 helix: 0.51 (0.25), residues: 435 sheet: -0.56 (0.22), residues: 594 loop : -1.25 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 686 HIS 0.006 0.001 HIS d 107 PHE 0.019 0.002 PHE c 296 TYR 0.018 0.002 TYR d 646 ARG 0.004 0.001 ARG c 330 *********************** 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 193 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 135 time to evaluate : 2.307 Fit side-chains REVERT: d 28 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8224 (mp) REVERT: d 217 LYS cc_start: 0.6533 (mppt) cc_final: 0.6212 (ttmt) REVERT: d 281 ASP cc_start: 0.8110 (t0) cc_final: 0.7872 (t70) REVERT: d 306 ASP cc_start: 0.7880 (t70) cc_final: 0.7569 (t70) REVERT: d 633 SER cc_start: 0.7970 (t) cc_final: 0.7569 (p) REVERT: j 1096 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7949 (mmmm) REVERT: h 1090 THR cc_start: 0.7931 (m) cc_final: 0.7456 (p) REVERT: i 1095 GLN cc_start: 0.7695 (tp40) cc_final: 0.7428 (tp-100) REVERT: i 1110 SER cc_start: 0.8709 (m) cc_final: 0.8500 (t) REVERT: c 338 MET cc_start: 0.8137 (ttp) cc_final: 0.7890 (ttp) REVERT: c 521 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7320 (p0) REVERT: c 579 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: c 605 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7291 (pp) REVERT: c 611 SER cc_start: 0.7495 (m) cc_final: 0.7058 (t) REVERT: b 143 ASN cc_start: 0.7589 (m110) cc_final: 0.6985 (t0) REVERT: b 198 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: b 499 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: b 554 ASN cc_start: 0.8221 (t0) cc_final: 0.7840 (t0) REVERT: b 608 LYS cc_start: 0.7843 (mttm) cc_final: 0.7079 (mttt) REVERT: b 664 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8525 (m) REVERT: b 675 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: b 695 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7237 (tp30) outliers start: 58 outliers final: 46 residues processed: 187 average time/residue: 0.2711 time to fit residues: 82.2060 Evaluate side-chains 181 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 126 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 318 ASP Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 529 THR 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 j residue 1118 ILE Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 47 ASP Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 398 ASN Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 521 ASN 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 47 ASP 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 499 GLU Chi-restraints excluded: chain b residue 515 ASN Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Chi-restraints excluded: chain b residue 695 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 94 GLN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 360 ASN c 398 ASN c 528 ASN b 51 ASN b 228 GLN b 528 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18702 Z= 0.193 Angle : 0.480 8.481 25314 Z= 0.260 Chirality : 0.045 0.193 2757 Planarity : 0.003 0.039 3279 Dihedral : 4.478 23.920 2520 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.98 % Allowed : 16.00 % 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: -1.04 (0.17), residues: 2277 helix: 0.58 (0.26), residues: 435 sheet: -0.27 (0.23), residues: 531 loop : -1.34 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 369 HIS 0.003 0.001 HIS d 107 PHE 0.016 0.001 PHE c 296 TYR 0.014 0.001 TYR d 646 ARG 0.004 0.000 ARG c 330 *********************** 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 202 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 142 time to evaluate : 2.268 Fit side-chains REVERT: d 217 LYS cc_start: 0.6538 (mppt) cc_final: 0.6233 (ttmt) REVERT: d 281 ASP cc_start: 0.8030 (t0) cc_final: 0.7756 (t70) REVERT: d 306 ASP cc_start: 0.7911 (t70) cc_final: 0.7565 (t70) REVERT: d 546 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6819 (mm-30) REVERT: d 633 SER cc_start: 0.7944 (t) cc_final: 0.7568 (p) REVERT: j 1090 THR cc_start: 0.7525 (m) cc_final: 0.7098 (p) REVERT: j 1096 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7916 (mmmm) REVERT: h 1090 THR cc_start: 0.7846 (m) cc_final: 0.7359 (p) REVERT: i 1095 GLN cc_start: 0.7736 (tp40) cc_final: 0.7457 (tp-100) REVERT: i 1102 MET cc_start: 0.7823 (mtt) cc_final: 0.7578 (mtt) REVERT: i 1110 SER cc_start: 0.8716 (m) cc_final: 0.8482 (t) REVERT: c 1 MET cc_start: 0.6574 (ppp) cc_final: 0.6334 (ttp) REVERT: c 338 MET cc_start: 0.8064 (ttp) cc_final: 0.7833 (ttp) REVERT: c 465 MET cc_start: 0.8401 (tpp) cc_final: 0.7990 (mmm) REVERT: c 521 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7162 (p0) REVERT: c 579 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: c 605 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7278 (pp) REVERT: c 611 SER cc_start: 0.7445 (m) cc_final: 0.7014 (t) REVERT: b 143 ASN cc_start: 0.7555 (m110) cc_final: 0.6974 (t0) REVERT: b 198 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: b 436 GLU cc_start: 0.6329 (mt-10) cc_final: 0.6011 (mt-10) REVERT: b 461 ILE cc_start: 0.8520 (mm) cc_final: 0.8274 (mt) REVERT: b 554 ASN cc_start: 0.8165 (t0) cc_final: 0.7720 (t0) REVERT: b 608 LYS cc_start: 0.7790 (mttm) cc_final: 0.7063 (mttt) REVERT: b 664 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8481 (m) REVERT: b 675 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: b 695 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7205 (tp30) outliers start: 60 outliers final: 42 residues processed: 193 average time/residue: 0.2832 time to fit residues: 86.6477 Evaluate side-chains 184 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 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 j residue 1118 ILE Chi-restraints excluded: chain h residue 1089 LEU 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 382 VAL Chi-restraints excluded: chain c residue 398 ASN Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 521 ASN 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 47 ASP 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 515 ASN Chi-restraints excluded: chain b residue 630 LEU Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Chi-restraints excluded: chain b residue 695 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 398 ASN c 528 ASN c 591 ASN b 51 ASN b 228 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18702 Z= 0.231 Angle : 0.500 9.617 25314 Z= 0.269 Chirality : 0.045 0.194 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.514 23.973 2520 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.88 % Allowed : 16.10 % 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: -1.00 (0.17), residues: 2277 helix: 0.77 (0.26), residues: 417 sheet: -0.30 (0.23), residues: 531 loop : -1.32 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 369 HIS 0.004 0.001 HIS b 339 PHE 0.016 0.001 PHE c 296 TYR 0.014 0.001 TYR d 646 ARG 0.004 0.000 ARG c 330 *********************** 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 198 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 140 time to evaluate : 1.549 Fit side-chains REVERT: d 217 LYS cc_start: 0.6524 (mppt) cc_final: 0.6243 (ttmt) REVERT: d 281 ASP cc_start: 0.8034 (t0) cc_final: 0.7752 (t70) REVERT: d 306 ASP cc_start: 0.7925 (t70) cc_final: 0.7520 (t70) REVERT: d 633 SER cc_start: 0.7954 (t) cc_final: 0.7549 (p) REVERT: j 1090 THR cc_start: 0.7529 (m) cc_final: 0.7120 (p) REVERT: j 1096 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7897 (mmmm) REVERT: h 1090 THR cc_start: 0.7826 (m) cc_final: 0.7344 (p) REVERT: i 1095 GLN cc_start: 0.7737 (tp40) cc_final: 0.7458 (tp-100) REVERT: i 1102 MET cc_start: 0.7839 (mtt) cc_final: 0.7600 (mtt) REVERT: i 1110 SER cc_start: 0.8742 (m) cc_final: 0.8496 (t) REVERT: c 1 MET cc_start: 0.6582 (ppp) cc_final: 0.6341 (ttp) REVERT: c 338 MET cc_start: 0.8062 (ttp) cc_final: 0.7833 (ttp) REVERT: c 521 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7140 (p0) REVERT: c 554 ASN cc_start: 0.8548 (t0) cc_final: 0.7882 (t0) REVERT: c 579 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: c 605 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7288 (pp) REVERT: c 611 SER cc_start: 0.7482 (m) cc_final: 0.7039 (t) REVERT: b 143 ASN cc_start: 0.7549 (m110) cc_final: 0.6965 (t0) REVERT: b 198 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: b 436 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5944 (mt-10) REVERT: b 461 ILE cc_start: 0.8554 (mm) cc_final: 0.8314 (mt) REVERT: b 554 ASN cc_start: 0.8159 (t0) cc_final: 0.7712 (t0) REVERT: b 608 LYS cc_start: 0.7800 (mttm) cc_final: 0.7076 (mttt) REVERT: b 664 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8476 (m) REVERT: b 675 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: b 695 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7224 (tp30) outliers start: 58 outliers final: 46 residues processed: 192 average time/residue: 0.2062 time to fit residues: 64.6037 Evaluate side-chains 186 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 318 ASP Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 428 THR Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 448 ASP Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 664 VAL Chi-restraints excluded: chain d residue 680 THR Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1089 LEU Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1089 LEU Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 521 ASN 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 47 ASP 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 253 VAL Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 515 ASN Chi-restraints excluded: chain b residue 582 LEU Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Chi-restraints excluded: chain b residue 695 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 18 optimal weight: 0.0470 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 398 ASN c 528 ASN c 591 ASN b 51 ASN b 228 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18702 Z= 0.145 Angle : 0.455 6.933 25314 Z= 0.246 Chirality : 0.044 0.191 2757 Planarity : 0.003 0.038 3279 Dihedral : 4.197 23.242 2520 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.63 % Allowed : 16.49 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.17), residues: 2277 helix: 0.73 (0.26), residues: 435 sheet: -0.18 (0.23), residues: 528 loop : -1.19 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 369 HIS 0.003 0.001 HIS b 339 PHE 0.014 0.001 PHE c 296 TYR 0.012 0.001 TYR d 646 ARG 0.004 0.000 ARG c 330 ********************** 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 195 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 142 time to evaluate : 2.090 Fit side-chains REVERT: d 217 LYS cc_start: 0.6459 (mppt) cc_final: 0.6201 (ttmt) REVERT: d 281 ASP cc_start: 0.7926 (t0) cc_final: 0.7653 (t70) REVERT: d 306 ASP cc_start: 0.7787 (t70) cc_final: 0.7387 (t70) REVERT: d 546 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (mm-30) REVERT: d 633 SER cc_start: 0.7944 (t) cc_final: 0.7557 (p) REVERT: j 1090 THR cc_start: 0.7398 (m) cc_final: 0.6998 (p) REVERT: j 1096 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7777 (mmmm) REVERT: h 1090 THR cc_start: 0.7672 (m) cc_final: 0.7198 (p) REVERT: i 1095 GLN cc_start: 0.7798 (tp40) cc_final: 0.7520 (tp-100) REVERT: i 1110 SER cc_start: 0.8662 (m) cc_final: 0.8440 (t) REVERT: c 1 MET cc_start: 0.6483 (ppp) cc_final: 0.6219 (ttp) REVERT: c 47 ASP cc_start: 0.8400 (m-30) cc_final: 0.7991 (p0) REVERT: c 338 MET cc_start: 0.8065 (ttp) cc_final: 0.7745 (ttp) REVERT: c 465 MET cc_start: 0.8357 (tpp) cc_final: 0.8015 (mmm) REVERT: c 554 ASN cc_start: 0.8499 (t0) cc_final: 0.7789 (t0) REVERT: c 579 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8258 (m-10) REVERT: c 605 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7336 (pp) REVERT: c 611 SER cc_start: 0.7413 (m) cc_final: 0.6979 (t) REVERT: b 143 ASN cc_start: 0.7668 (m110) cc_final: 0.7156 (t0) REVERT: b 251 LYS cc_start: 0.4391 (tttt) cc_final: 0.3837 (tttt) REVERT: b 336 ASP cc_start: 0.6947 (m-30) cc_final: 0.6720 (t0) REVERT: b 436 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6110 (mt-10) REVERT: b 461 ILE cc_start: 0.8500 (mm) cc_final: 0.8269 (mt) REVERT: b 499 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: b 554 ASN cc_start: 0.8063 (t0) cc_final: 0.7214 (t0) REVERT: b 608 LYS cc_start: 0.7738 (mttm) cc_final: 0.7056 (mttt) REVERT: b 675 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: b 695 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7247 (tp30) outliers start: 53 outliers final: 42 residues processed: 189 average time/residue: 0.2717 time to fit residues: 82.3709 Evaluate side-chains 182 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 146 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 290 VAL Chi-restraints excluded: chain d residue 318 ASP Chi-restraints excluded: chain d residue 382 VAL Chi-restraints excluded: chain d residue 442 VAL Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 529 THR Chi-restraints excluded: chain d residue 661 SER Chi-restraints excluded: chain d residue 717 ILE Chi-restraints excluded: chain j residue 1109 LEU Chi-restraints excluded: chain j residue 1118 ILE Chi-restraints excluded: chain h residue 1110 SER Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 THR Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 333 ILE Chi-restraints excluded: chain c residue 382 VAL Chi-restraints excluded: chain c residue 437 VAL Chi-restraints excluded: chain c residue 448 ASP Chi-restraints excluded: chain c residue 451 ILE Chi-restraints excluded: chain c residue 579 TYR Chi-restraints excluded: chain c residue 591 ASN 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 104 ILE Chi-restraints excluded: chain b residue 146 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 397 GLN Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 451 ILE Chi-restraints excluded: chain b residue 497 ILE Chi-restraints excluded: chain b residue 499 GLU Chi-restraints excluded: chain b residue 515 ASN Chi-restraints excluded: chain b residue 664 VAL Chi-restraints excluded: chain b residue 675 ASP Chi-restraints excluded: chain b residue 695 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 349 GLN d 569 ASN ** c 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 398 ASN c 528 ASN ** c 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 68 GLN b 228 GLN b 400 ASN b 528 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.086243 restraints weight = 29424.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.086328 restraints weight = 20106.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.087087 restraints weight = 17393.687| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18702 Z= 0.389 Angle : 0.596 10.598 25314 Z= 0.318 Chirality : 0.048 0.231 2757 Planarity : 0.004 0.055 3279 Dihedral : 4.912 24.928 2520 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.98 % Allowed : 16.24 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.25), residues: 435 sheet: -0.39 (0.23), residues: 540 loop : -1.42 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP d 156 HIS 0.006 0.002 HIS d 107 PHE 0.020 0.002 PHE c 296 TYR 0.025 0.002 TYR b 646 ARG 0.005 0.001 ARG c 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.46 seconds wall clock time: 57 minutes 36.47 seconds (3456.47 seconds total)