Starting phenix.real_space_refine on Sun Feb 18 06:04:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvv_23543/02_2024/7lvv_23543_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 110 5.49 5 S 44 5.16 5 C 12960 2.51 5 N 3709 2.21 5 O 4193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A ARG 988": "NH1" <-> "NH2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A ARG 1002": "NH1" <-> "NH2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 870": "NH1" <-> "NH2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B GLU 912": "OE1" <-> "OE2" Residue "B ASP 935": "OD1" <-> "OD2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B GLU 975": "OE1" <-> "OE2" Residue "B ASP 984": "OD1" <-> "OD2" Residue "B ARG 988": "NH1" <-> "NH2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B ASP 1005": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21020 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8216 Classifications: {'peptide': 1011} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 969} Chain breaks: 2 Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8219 Classifications: {'peptide': 1012} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 970} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.23, per 1000 atoms: 0.53 Number of scatterers: 21020 At special positions: 0 Unit cell: (106.72, 107.88, 203, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 44 16.00 P 110 15.00 O 4193 8.00 N 3709 7.00 C 12960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 3.8 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 14 sheets defined 41.7% alpha, 6.8% beta 48 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 10.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.703A pdb=" N GLY A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.573A pdb=" N ALA A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.710A pdb=" N ILE A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.876A pdb=" N ASP A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.582A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 233 through 242 removed outlier: 4.226A pdb=" N LEU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.177A pdb=" N ARG A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.576A pdb=" N ARG A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.606A pdb=" N THR A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.699A pdb=" N GLU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.585A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 523 through 531 removed outlier: 4.304A pdb=" N GLY A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 683 through 702 removed outlier: 3.647A pdb=" N ASN A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 987 through 990 No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 1001 through 1023 Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.523A pdb=" N PHE B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 14 " --> pdb=" O GLN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 43 removed outlier: 4.904A pdb=" N ALA B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.880A pdb=" N GLN B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 145 through 177 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 196 Processing helix chain 'B' and resid 202 through 219 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 248 through 270 removed outlier: 4.201A pdb=" N ARG B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.504A pdb=" N ARG B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 308 through 325 removed outlier: 3.535A pdb=" N LYS B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 removed outlier: 4.265A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.550A pdb=" N ARG B 472 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG B 473 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 475 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 492 through 503 removed outlier: 3.640A pdb=" N ARG B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'B' and resid 527 through 533 removed outlier: 5.050A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.725A pdb=" N LYS B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 685 through 701 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 766 through 768 No H-bonds generated for 'chain 'B' and resid 766 through 768' Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 828 through 837 Processing helix chain 'B' and resid 845 through 857 Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 866 through 869 No H-bonds generated for 'chain 'B' and resid 866 through 869' Processing helix chain 'B' and resid 882 through 897 removed outlier: 3.835A pdb=" N TRP B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 889 " --> pdb=" O TRP B 885 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 890 " --> pdb=" O ALA B 886 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 923 Processing helix chain 'B' and resid 969 through 976 Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 996 through 1023 removed outlier: 6.475A pdb=" N GLU B1001 " --> pdb=" O ASP B 998 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1008 " --> pdb=" O ASP B1005 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B1010 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B1020 " --> pdb=" O THR B1017 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1021 " --> pdb=" O VAL B1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.510A pdb=" N ALA C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 43 removed outlier: 4.786A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 4.304A pdb=" N GLN C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 Processing helix chain 'D' and resid 6 through 9 No H-bonds generated for 'chain 'D' and resid 6 through 9' Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.724A pdb=" N ILE D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 43 removed outlier: 5.034A pdb=" N ALA D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 43 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 97 Processing helix chain 'D' and resid 129 through 141 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.889A pdb=" N ILE A 104 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 508 through 515 removed outlier: 3.570A pdb=" N GLY A 508 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 510 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.655A pdb=" N GLN A 809 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 943 through 945 Processing sheet with id= E, first strand: chain 'A' and resid 740 through 746 removed outlier: 6.863A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 49 removed outlier: 3.541A pdb=" N GLY B 76 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 104 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 368 through 370 removed outlier: 6.434A pdb=" N ILE B 337 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 338 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE B 445 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 508 through 514 removed outlier: 6.287A pdb=" N LYS B 589 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 540 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TRP B 591 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP B 542 " --> pdb=" O TRP B 591 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS B 593 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 793 through 796 Processing sheet with id= J, first strand: chain 'B' and resid 814 through 816 Processing sheet with id= K, first strand: chain 'B' and resid 908 through 911 Processing sheet with id= L, first strand: chain 'B' and resid 740 through 746 removed outlier: 6.660A pdb=" N ASP B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.761A pdb=" N GLN C 122 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN C 116 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.628A pdb=" N GLU D 107 " --> pdb=" O GLU D 79 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3415 1.31 - 1.44: 6258 1.44 - 1.57: 11709 1.57 - 1.70: 213 1.70 - 1.83: 86 Bond restraints: 21681 Sorted by residual: bond pdb=" C ASN A 712 " pdb=" N TRP A 713 " ideal model delta sigma weight residual 1.332 1.247 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C SER B 844 " pdb=" N ARG B 845 " ideal model delta sigma weight residual 1.335 1.263 0.072 1.25e-02 6.40e+03 3.31e+01 bond pdb=" C VAL A 741 " pdb=" N PRO A 742 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.20e-02 6.94e+03 3.02e+01 bond pdb=" C LYS A 702 " pdb=" N LEU A 703 " ideal model delta sigma weight residual 1.328 1.405 -0.077 1.44e-02 4.82e+03 2.85e+01 bond pdb=" C PRO B 144 " pdb=" O PRO B 144 " ideal model delta sigma weight residual 1.240 1.182 0.058 1.12e-02 7.97e+03 2.69e+01 ... (remaining 21676 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.24: 988 105.24 - 112.57: 10052 112.57 - 119.89: 10439 119.89 - 127.22: 7911 127.22 - 134.54: 381 Bond angle restraints: 29771 Sorted by residual: angle pdb=" N ILE A 987 " pdb=" CA ILE A 987 " pdb=" C ILE A 987 " ideal model delta sigma weight residual 113.47 104.56 8.91 1.01e+00 9.80e-01 7.79e+01 angle pdb=" N GLU B 299 " pdb=" CA GLU B 299 " pdb=" C GLU B 299 " ideal model delta sigma weight residual 114.04 103.10 10.94 1.24e+00 6.50e-01 7.78e+01 angle pdb=" N GLN B 728 " pdb=" CA GLN B 728 " pdb=" C GLN B 728 " ideal model delta sigma weight residual 112.72 102.92 9.80 1.14e+00 7.69e-01 7.40e+01 angle pdb=" N ARG A 929 " pdb=" CA ARG A 929 " pdb=" C ARG A 929 " ideal model delta sigma weight residual 112.97 104.07 8.90 1.06e+00 8.90e-01 7.04e+01 angle pdb=" C LYS A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 123.07 110.94 12.13 1.46e+00 4.69e-01 6.91e+01 ... (remaining 29766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 11273 32.96 - 65.91: 1469 65.91 - 98.87: 60 98.87 - 131.83: 1 131.83 - 164.78: 2 Dihedral angle restraints: 12805 sinusoidal: 6033 harmonic: 6772 Sorted by residual: dihedral pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual 122.80 140.99 -18.19 0 2.50e+00 1.60e-01 5.29e+01 dihedral pdb=" C ASP C 69 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " pdb=" CB ASP C 69 " ideal model delta harmonic sigma weight residual -122.60 -139.94 17.34 0 2.50e+00 1.60e-01 4.81e+01 dihedral pdb=" C GLN B 33 " pdb=" N GLN B 33 " pdb=" CA GLN B 33 " pdb=" CB GLN B 33 " ideal model delta harmonic sigma weight residual -122.60 -107.31 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 12802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2554 0.149 - 0.298: 629 0.298 - 0.448: 31 0.448 - 0.597: 0 0.597 - 0.746: 1 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CA ASP C 69 " pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CB ASP C 69 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP A 88 " pdb=" N ASP A 88 " pdb=" C ASP A 88 " pdb=" CB ASP A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA THR C 49 " pdb=" N THR C 49 " pdb=" C THR C 49 " pdb=" CB THR C 49 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3212 not shown) Planarity restraints: 3504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 926 " -0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C LYS B 926 " 0.098 2.00e-02 2.50e+03 pdb=" O LYS B 926 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS B 927 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 646 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C ALA B 646 " -0.094 2.00e-02 2.50e+03 pdb=" O ALA B 646 " 0.036 2.00e-02 2.50e+03 pdb=" N ASP B 647 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 43 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C SER D 43 " -0.092 2.00e-02 2.50e+03 pdb=" O SER D 43 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY D 44 " 0.032 2.00e-02 2.50e+03 ... (remaining 3501 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 28 2.34 - 2.98: 10860 2.98 - 3.62: 31047 3.62 - 4.26: 55627 4.26 - 4.90: 84629 Nonbonded interactions: 182191 Sorted by model distance: nonbonded pdb=" OE2 GLU D 25 " pdb="CA CA D1101 " model vdw 1.705 2.510 nonbonded pdb=" OD1 ASP B 64 " pdb="CA CA B1102 " model vdw 1.754 2.510 nonbonded pdb=" OP1 DG F 9 " pdb="CA CA C1101 " model vdw 1.874 2.510 nonbonded pdb=" OP1 DG H 9 " pdb="CA CA D1101 " model vdw 2.036 2.510 nonbonded pdb=" OD1 ASP D 69 " pdb=" N SER D 70 " model vdw 2.074 2.520 ... (remaining 182186 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 'A' and (resid 2 through 578 or resid 587 through 1029 or resid 1101 thro \ ugh 1102)) selection = (chain 'B' and (resid 2 through 411 or resid 422 through 1029 or resid 1101 thro \ ugh 1102)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 144 or resid 1101)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.260 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 66.730 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.013 0.085 21681 Z= 0.806 Angle : 1.795 12.133 29771 Z= 1.309 Chirality : 0.119 0.746 3215 Planarity : 0.007 0.080 3504 Dihedral : 23.618 164.782 8433 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 1.31 % Allowed : 10.32 % Favored : 88.37 % Rotamer: Outliers : 13.97 % Allowed : 16.78 % Favored : 69.25 % Cbeta Deviations : 1.46 % Peptide Plane: Cis-proline : 2.25 % 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: -4.96 (0.13), residues: 2296 helix: -3.06 (0.12), residues: 1029 sheet: -3.38 (0.35), residues: 138 loop : -3.53 (0.14), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 39 HIS 0.012 0.002 HIS B 858 PHE 0.028 0.003 PHE A 326 TYR 0.037 0.003 TYR A 573 ARG 0.005 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 507 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7358 (mmt90) REVERT: A 52 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8045 (t) REVERT: A 185 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8446 (tmm-80) REVERT: A 237 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8178 (tp-100) REVERT: A 366 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: A 451 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: A 629 TRP cc_start: 0.8505 (m-10) cc_final: 0.8172 (m-10) REVERT: A 641 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.4805 (mm-30) REVERT: A 1024 MET cc_start: 0.8023 (mtt) cc_final: 0.7531 (mtm) REVERT: B 188 PHE cc_start: 0.7504 (t80) cc_final: 0.7285 (t80) REVERT: B 246 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: B 319 ASP cc_start: 0.8007 (t0) cc_final: 0.7370 (t0) REVERT: B 328 LYS cc_start: 0.8652 (mttt) cc_final: 0.7481 (mmtm) REVERT: B 472 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7578 (tmm160) REVERT: B 512 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: B 649 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: B 713 TRP cc_start: 0.6846 (p-90) cc_final: 0.6608 (p-90) REVERT: B 792 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: B 831 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (tt) REVERT: B 857 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8385 (m90) REVERT: B 876 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 983 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (mmtm) REVERT: B 986 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9253 (p) REVERT: C 25 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: C 86 THR cc_start: 0.8651 (m) cc_final: 0.8390 (p) REVERT: D 88 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8137 (t70) REVERT: D 94 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5429 (mmtm) REVERT: D 132 LEU cc_start: 0.7770 (tp) cc_final: 0.7562 (tp) outliers start: 274 outliers final: 32 residues processed: 713 average time/residue: 0.4496 time to fit residues: 449.2779 Evaluate side-chains 293 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 241 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 983 LYS Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1018 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 212 HIS A 232 ASN A 288 ASN A 325 HIS ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 464 ASN A 673 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 116 GLN B 229 HIS B 232 ASN B 233 ASN B 266 GLN B 288 ASN B 448 ASN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 620 HIS B 763 GLN B 765 GLN B 792 GLN B 824 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 60 ASN C 72 GLN D 10 GLN D 24 ASN D 59 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21681 Z= 0.226 Angle : 0.674 8.434 29771 Z= 0.367 Chirality : 0.042 0.170 3215 Planarity : 0.005 0.059 3504 Dihedral : 22.918 172.181 3902 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 4.23 % Allowed : 21.26 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.16), residues: 2296 helix: -1.09 (0.15), residues: 1047 sheet: -2.32 (0.37), residues: 166 loop : -2.57 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.010 0.001 HIS A 325 PHE 0.024 0.002 PHE B 882 TYR 0.017 0.001 TYR A 814 ARG 0.008 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 262 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7625 (tt0) cc_final: 0.7332 (mt0) REVERT: A 52 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7997 (t) REVERT: A 115 MET cc_start: 0.7348 (tpp) cc_final: 0.7115 (tpp) REVERT: A 185 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8614 (tmm-80) REVERT: A 766 MET cc_start: 0.8686 (tpp) cc_final: 0.8429 (tpp) REVERT: B 648 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8747 (pttt) REVERT: B 664 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8078 (tptp) REVERT: C 120 GLU cc_start: 0.8247 (tt0) cc_final: 0.7984 (tt0) REVERT: C 123 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6956 (ttm-80) REVERT: D 82 ASP cc_start: 0.0794 (OUTLIER) cc_final: 0.0436 (p0) REVERT: D 136 LEU cc_start: 0.7307 (mt) cc_final: 0.6735 (pp) REVERT: D 141 GLU cc_start: 0.6096 (mt-10) cc_final: 0.5216 (pp20) outliers start: 83 outliers final: 38 residues processed: 332 average time/residue: 0.3862 time to fit residues: 190.4374 Evaluate side-chains 238 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 666 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 105 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 179 optimal weight: 0.0060 chunk 147 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 214 optimal weight: 0.0980 chunk 73 optimal weight: 0.9990 chunk 173 optimal weight: 0.0770 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 712 ASN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 266 GLN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS B 628 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21681 Z= 0.171 Angle : 0.579 10.162 29771 Z= 0.312 Chirality : 0.040 0.191 3215 Planarity : 0.004 0.044 3504 Dihedral : 22.023 178.138 3828 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 3.06 % Allowed : 22.03 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.94 (0.17), residues: 2296 helix: -0.25 (0.16), residues: 1050 sheet: -1.95 (0.35), residues: 187 loop : -2.25 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 39 HIS 0.006 0.001 HIS B 620 PHE 0.016 0.001 PHE B 882 TYR 0.014 0.001 TYR A 451 ARG 0.015 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7635 (tt0) cc_final: 0.7349 (mt0) REVERT: A 46 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7179 (mmt90) REVERT: A 115 MET cc_start: 0.7367 (tpp) cc_final: 0.7122 (tpp) REVERT: A 185 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8520 (tmm-80) REVERT: A 316 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: A 680 SER cc_start: 0.7007 (OUTLIER) cc_final: 0.6564 (p) REVERT: B 11 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7878 (ttpp) REVERT: B 69 ASP cc_start: 0.7278 (p0) cc_final: 0.6979 (p0) REVERT: B 246 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6782 (m-10) REVERT: B 628 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 649 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: B 664 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8088 (tptp) REVERT: B 762 MET cc_start: 0.8149 (mmm) cc_final: 0.7848 (mmt) REVERT: D 3 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7156 (tp) REVERT: D 136 LEU cc_start: 0.7458 (mt) cc_final: 0.6776 (pp) outliers start: 60 outliers final: 23 residues processed: 267 average time/residue: 0.3596 time to fit residues: 145.1736 Evaluate side-chains 212 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 0.4980 chunk 230 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 620 HIS B 652 GLN B 712 ASN B 758 ASN ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 103 ASN D 72 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 21681 Z= 0.396 Angle : 0.699 10.113 29771 Z= 0.376 Chirality : 0.044 0.167 3215 Planarity : 0.005 0.059 3504 Dihedral : 21.789 175.324 3811 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 4.33 % Allowed : 21.06 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.65 (0.17), residues: 2296 helix: -0.07 (0.16), residues: 1050 sheet: -1.44 (0.32), residues: 224 loop : -2.11 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 599 HIS 0.009 0.002 HIS B 275 PHE 0.024 0.002 PHE D 140 TYR 0.020 0.002 TYR B 396 ARG 0.009 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 194 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7783 (tt0) cc_final: 0.7434 (mt0) REVERT: A 115 MET cc_start: 0.7450 (tpp) cc_final: 0.7179 (tpp) REVERT: A 326 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: A 709 MET cc_start: 0.7538 (ppp) cc_final: 0.7165 (ppp) REVERT: B 246 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: B 649 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: B 664 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8221 (tptp) REVERT: C 19 TYR cc_start: 0.8957 (m-80) cc_final: 0.8755 (m-10) REVERT: C 22 THR cc_start: 0.8768 (m) cc_final: 0.8385 (p) REVERT: C 93 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8296 (mtmm) REVERT: C 120 GLU cc_start: 0.8344 (tt0) cc_final: 0.8100 (tt0) REVERT: C 123 ARG cc_start: 0.7171 (ttm-80) cc_final: 0.6924 (ttm-80) REVERT: D 3 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7936 (tp) REVERT: D 83 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6505 (mm-30) REVERT: D 141 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6203 (pt0) outliers start: 85 outliers final: 46 residues processed: 263 average time/residue: 0.3797 time to fit residues: 149.6760 Evaluate side-chains 221 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 170 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 163 HIS B 279 GLN B 362 GLN B 560 ASN B 620 HIS B 837 HIS ** B 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS C 53 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21681 Z= 0.198 Angle : 0.570 8.626 29771 Z= 0.305 Chirality : 0.039 0.171 3215 Planarity : 0.004 0.044 3504 Dihedral : 21.550 178.002 3805 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.01 % Allowed : 22.34 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.17), residues: 2296 helix: 0.24 (0.16), residues: 1055 sheet: -1.22 (0.33), residues: 213 loop : -1.91 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 960 HIS 0.005 0.001 HIS B 620 PHE 0.020 0.001 PHE C 142 TYR 0.018 0.001 TYR A 814 ARG 0.005 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 195 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7701 (tt0) cc_final: 0.7358 (mt0) REVERT: A 115 MET cc_start: 0.7465 (tpp) cc_final: 0.7212 (tpp) REVERT: A 326 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: B 115 MET cc_start: 0.7964 (ttt) cc_final: 0.7726 (ttt) REVERT: B 246 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: B 362 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: B 628 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (p0) REVERT: B 649 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: B 719 MET cc_start: 0.8542 (mmm) cc_final: 0.8148 (mmm) REVERT: B 762 MET cc_start: 0.8062 (mmm) cc_final: 0.7631 (mmt) REVERT: B 960 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7959 (m100) REVERT: C 22 THR cc_start: 0.8591 (m) cc_final: 0.8276 (p) REVERT: C 123 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.7015 (ttm-80) REVERT: D 83 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6439 (mm-30) REVERT: D 141 GLU cc_start: 0.6428 (mt-10) cc_final: 0.5232 (pp20) outliers start: 59 outliers final: 34 residues processed: 241 average time/residue: 0.3639 time to fit residues: 132.4451 Evaluate side-chains 215 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 45 optimal weight: 0.0070 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 120 optimal weight: 6.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 229 HIS B 620 HIS B 858 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21681 Z= 0.180 Angle : 0.555 9.822 29771 Z= 0.296 Chirality : 0.038 0.203 3215 Planarity : 0.004 0.044 3504 Dihedral : 21.355 177.750 3801 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.91 % Allowed : 22.69 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 2296 helix: 0.40 (0.16), residues: 1069 sheet: -1.08 (0.33), residues: 219 loop : -1.81 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 960 HIS 0.005 0.001 HIS B 620 PHE 0.021 0.001 PHE C 142 TYR 0.017 0.001 TYR B 305 ARG 0.008 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7694 (tt0) cc_final: 0.7378 (mt0) REVERT: A 46 ARG cc_start: 0.7912 (mmt-90) cc_final: 0.7210 (mmt90) REVERT: A 709 MET cc_start: 0.7702 (ppp) cc_final: 0.7485 (ppp) REVERT: B 168 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9192 (mm) REVERT: B 246 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: B 719 MET cc_start: 0.8535 (mmm) cc_final: 0.8288 (mmm) REVERT: B 960 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7988 (m100) REVERT: C 22 THR cc_start: 0.8689 (m) cc_final: 0.8381 (p) REVERT: D 25 GLU cc_start: 0.6806 (tt0) cc_final: 0.6038 (pt0) REVERT: D 83 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6570 (mm-30) outliers start: 57 outliers final: 41 residues processed: 225 average time/residue: 0.3757 time to fit residues: 128.2284 Evaluate side-chains 212 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 448 ASN B 620 HIS B 977 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21681 Z= 0.282 Angle : 0.598 15.790 29771 Z= 0.316 Chirality : 0.040 0.168 3215 Planarity : 0.004 0.044 3504 Dihedral : 21.338 176.525 3798 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 3.62 % Allowed : 22.08 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.90 (0.17), residues: 2296 helix: 0.52 (0.16), residues: 1052 sheet: -1.01 (0.34), residues: 223 loop : -1.70 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 960 HIS 0.006 0.001 HIS A 537 PHE 0.018 0.002 PHE C 142 TYR 0.019 0.001 TYR C 77 ARG 0.007 0.001 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 173 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.7464 (tpp) cc_final: 0.7254 (tpp) REVERT: A 326 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: B 246 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8197 (m-10) REVERT: B 719 MET cc_start: 0.8650 (mmm) cc_final: 0.8302 (mmm) REVERT: B 762 MET cc_start: 0.8181 (mmm) cc_final: 0.7627 (mmt) REVERT: B 960 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7973 (m100) REVERT: C 22 THR cc_start: 0.8731 (m) cc_final: 0.8397 (p) REVERT: C 93 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8537 (mtmm) REVERT: D 82 ASP cc_start: 0.0963 (OUTLIER) cc_final: 0.0708 (p0) REVERT: D 83 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6621 (mm-30) outliers start: 71 outliers final: 51 residues processed: 225 average time/residue: 0.3619 time to fit residues: 124.6644 Evaluate side-chains 214 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 868 ASN Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 448 ASN B 620 HIS C 72 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21681 Z= 0.175 Angle : 0.566 12.902 29771 Z= 0.297 Chirality : 0.039 0.193 3215 Planarity : 0.004 0.044 3504 Dihedral : 21.155 177.424 3798 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.70 % Allowed : 23.25 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.83 (0.17), residues: 2296 helix: 0.52 (0.16), residues: 1064 sheet: -1.00 (0.33), residues: 234 loop : -1.61 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 888 HIS 0.007 0.001 HIS A 850 PHE 0.019 0.001 PHE C 142 TYR 0.020 0.001 TYR B 305 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7651 (m-80) cc_final: 0.7372 (m-10) REVERT: A 395 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5725 (ppt170) REVERT: A 762 MET cc_start: 0.7861 (mmm) cc_final: 0.7261 (mmt) REVERT: B 246 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: B 353 ASP cc_start: 0.8375 (t0) cc_final: 0.8060 (t0) REVERT: B 642 PHE cc_start: 0.7179 (t80) cc_final: 0.6696 (t80) REVERT: B 719 MET cc_start: 0.8674 (mmm) cc_final: 0.8312 (mmm) REVERT: B 762 MET cc_start: 0.8239 (mmm) cc_final: 0.7644 (mmt) REVERT: B 920 GLU cc_start: 0.7377 (mp0) cc_final: 0.6799 (mm-30) REVERT: B 960 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7851 (m100) REVERT: C 12 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.7396 (ptp-110) REVERT: C 22 THR cc_start: 0.8705 (m) cc_final: 0.8394 (p) REVERT: C 34 GLN cc_start: 0.8094 (tt0) cc_final: 0.7680 (tt0) REVERT: D 25 GLU cc_start: 0.6819 (tt0) cc_final: 0.5988 (pt0) outliers start: 53 outliers final: 36 residues processed: 214 average time/residue: 0.3651 time to fit residues: 119.1405 Evaluate side-chains 203 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21681 Z= 0.196 Angle : 0.571 12.482 29771 Z= 0.299 Chirality : 0.039 0.315 3215 Planarity : 0.004 0.042 3504 Dihedral : 21.086 176.822 3798 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.45 % Allowed : 23.51 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2296 helix: 0.59 (0.16), residues: 1062 sheet: -0.90 (0.33), residues: 236 loop : -1.54 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 888 HIS 0.008 0.001 HIS A 163 PHE 0.023 0.001 PHE C 142 TYR 0.020 0.001 TYR C 77 ARG 0.007 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5448 (ppt170) REVERT: A 762 MET cc_start: 0.7865 (mmm) cc_final: 0.7272 (mmt) REVERT: B 246 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: B 353 ASP cc_start: 0.8356 (t0) cc_final: 0.8017 (t0) REVERT: B 362 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8050 (tp40) REVERT: B 719 MET cc_start: 0.8697 (mmm) cc_final: 0.8383 (mmm) REVERT: B 762 MET cc_start: 0.8054 (mmm) cc_final: 0.7534 (mmt) REVERT: B 960 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.7947 (m100) REVERT: C 22 THR cc_start: 0.8756 (m) cc_final: 0.8453 (p) outliers start: 48 outliers final: 36 residues processed: 209 average time/residue: 0.3651 time to fit residues: 116.4609 Evaluate side-chains 200 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21681 Z= 0.174 Angle : 0.575 11.886 29771 Z= 0.300 Chirality : 0.039 0.309 3215 Planarity : 0.004 0.061 3504 Dihedral : 21.031 176.905 3798 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 2.04 % Allowed : 24.22 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.65 (0.18), residues: 2296 helix: 0.66 (0.17), residues: 1052 sheet: -0.79 (0.33), residues: 234 loop : -1.50 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 888 HIS 0.008 0.001 HIS A 850 PHE 0.023 0.001 PHE C 142 TYR 0.019 0.001 TYR B 305 ARG 0.019 0.000 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5499 (ppt170) REVERT: A 762 MET cc_start: 0.7859 (mmm) cc_final: 0.7248 (mmt) REVERT: B 246 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: B 353 ASP cc_start: 0.8306 (t0) cc_final: 0.8035 (t0) REVERT: B 362 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7762 (tp-100) REVERT: B 719 MET cc_start: 0.8698 (mmm) cc_final: 0.8374 (mmm) REVERT: B 762 MET cc_start: 0.8018 (mmm) cc_final: 0.7489 (mmt) REVERT: B 960 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7845 (m100) REVERT: C 22 THR cc_start: 0.8747 (m) cc_final: 0.8458 (p) REVERT: D 25 GLU cc_start: 0.6783 (tt0) cc_final: 0.5912 (pt0) outliers start: 40 outliers final: 33 residues processed: 199 average time/residue: 0.3680 time to fit residues: 111.6915 Evaluate side-chains 202 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 189 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.088354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070120 restraints weight = 66339.153| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.94 r_work: 0.3030 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21681 Z= 0.175 Angle : 0.575 11.660 29771 Z= 0.300 Chirality : 0.039 0.309 3215 Planarity : 0.004 0.061 3504 Dihedral : 21.003 176.838 3798 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 2.14 % Allowed : 24.12 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.59 (0.18), residues: 2296 helix: 0.69 (0.16), residues: 1053 sheet: -0.75 (0.33), residues: 242 loop : -1.47 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 888 HIS 0.008 0.001 HIS A 850 PHE 0.023 0.001 PHE C 142 TYR 0.019 0.001 TYR B 305 ARG 0.015 0.000 ARG C 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4742.98 seconds wall clock time: 86 minutes 55.31 seconds (5215.31 seconds total)