Starting phenix.real_space_refine on Mon Dec 30 20:27:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.map" model { file = "/net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tan_41138/12_2024/8tan_41138.cif" } resolution = 3.05 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 8738 2.51 5 N 2360 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13853 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6674 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 783} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6530 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 765} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 400 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.42, per 1000 atoms: 0.61 Number of scatterers: 13853 At special positions: 0 Unit cell: (91.16, 120.84, 172.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2653 8.00 N 2360 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 458 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 47 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 53 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 592 " " NAG A1002 " - " ASN A 610 " " NAG A1003 " - " ASN A 577 " " NAG A1004 " - " ASN A 504 " " NAG A1005 " - " ASN A 21 " " NAG A1006 " - " ASN A 408 " " NAG A1007 " - " ASN A 387 " " NAG B1001 " - " ASN B 504 " " NAG B1002 " - " ASN B 610 " " NAG B1003 " - " ASN B 21 " " NAG B1004 " - " ASN B 214 " " NAG D 1 " - " ASN A 105 " " NAG E 1 " - " ASN B 105 " " NAG F 1 " - " ASN B 592 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 34 sheets defined 16.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.530A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.756A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.635A pdb=" N CYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.299A pdb=" N MET A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.988A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.628A pdb=" N ASN A 448 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.719A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 703 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.699A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.590A pdb=" N TYR B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.197A pdb=" N GLU B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.080A pdb=" N GLU B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.238A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.349A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.564A pdb=" N ILE B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 625 through 630 removed outlier: 3.631A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 699 removed outlier: 3.802A pdb=" N PHE B 694 " --> pdb=" O TYR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 removed outlier: 3.554A pdb=" N LYS B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.500A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 57 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 6.360A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.893A pdb=" N THR A 165 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.634A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 247 removed outlier: 6.720A pdb=" N ARG A 240 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 281 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.254A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR A 417 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 391 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA A 419 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU A 393 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB2, first strand: chain 'A' and resid 465 through 470 removed outlier: 3.573A pdb=" N SER A 467 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.721A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB5, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.581A pdb=" N TYR A 613 " --> pdb=" O CYS A 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 809 through 812 Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AC1, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.177A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 163 through 167 removed outlier: 4.796A pdb=" N GLU B 163 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC4, first strand: chain 'B' and resid 245 through 247 removed outlier: 6.807A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AC6, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 311 removed outlier: 6.595A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 388 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR B 417 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 390 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA B 419 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 392 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC9, first strand: chain 'B' and resid 465 through 470 removed outlier: 3.681A pdb=" N SER B 467 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 520 through 525 Processing sheet with id=AD2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 752 removed outlier: 3.982A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 773 " --> pdb=" O ASN B 789 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 809 through 813 removed outlier: 3.579A pdb=" N SER B 817 " --> pdb=" O ARG B 813 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 846 through 851 Processing sheet with id=AD7, first strand: chain 'B' and resid 869 through 870 360 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4514 1.35 - 1.47: 3417 1.47 - 1.59: 6112 1.59 - 1.71: 0 1.71 - 1.84: 128 Bond restraints: 14171 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.589 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 ... (remaining 14166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18331 1.71 - 3.42: 784 3.42 - 5.13: 81 5.13 - 6.84: 10 6.84 - 8.55: 5 Bond angle restraints: 19211 Sorted by residual: angle pdb=" N GLU C 21 " pdb=" CA GLU C 21 " pdb=" C GLU C 21 " ideal model delta sigma weight residual 114.75 109.91 4.84 1.26e+00 6.30e-01 1.48e+01 angle pdb=" N ILE A 340 " pdb=" CA ILE A 340 " pdb=" C ILE A 340 " ideal model delta sigma weight residual 110.42 114.02 -3.60 9.40e-01 1.13e+00 1.47e+01 angle pdb=" C PHE A 241 " pdb=" N GLU A 242 " pdb=" CA GLU A 242 " ideal model delta sigma weight residual 122.08 127.16 -5.08 1.47e+00 4.63e-01 1.19e+01 angle pdb=" C HIS A 223 " pdb=" N TYR A 224 " pdb=" CA TYR A 224 " ideal model delta sigma weight residual 122.59 117.59 5.00 1.57e+00 4.06e-01 1.02e+01 angle pdb=" CA TRP B 402 " pdb=" CB TRP B 402 " pdb=" CG TRP B 402 " ideal model delta sigma weight residual 113.60 119.64 -6.04 1.90e+00 2.77e-01 1.01e+01 ... (remaining 19206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 8327 21.26 - 42.52: 443 42.52 - 63.78: 78 63.78 - 85.04: 25 85.04 - 106.30: 6 Dihedral angle restraints: 8879 sinusoidal: 3916 harmonic: 4963 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 849 " pdb=" CB CYS A 849 " ideal model delta sinusoidal sigma weight residual -86.00 -148.89 62.89 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual -86.00 -144.08 58.08 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS B 425 " pdb=" SG CYS B 425 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 143.95 -50.95 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1813 0.074 - 0.148: 286 0.148 - 0.223: 13 0.223 - 0.297: 3 0.297 - 0.371: 3 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 504 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 408 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG B1004 " pdb=" ND2 ASN B 214 " pdb=" C2 NAG B1004 " pdb=" O5 NAG B1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2115 not shown) Planarity restraints: 2489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 638 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 639 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 580 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 581 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 484 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 485 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.026 5.00e-02 4.00e+02 ... (remaining 2486 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 831 2.73 - 3.28: 13970 3.28 - 3.82: 22585 3.82 - 4.36: 29072 4.36 - 4.90: 47349 Nonbonded interactions: 113807 Sorted by model distance: nonbonded pdb=" O MET A 432 " pdb=" OG1 THR A 436 " model vdw 2.194 3.040 nonbonded pdb=" O PRO A 584 " pdb=" ND2 ASN A 789 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU B 26 " pdb=" NE ARG B 245 " model vdw 2.254 3.120 nonbonded pdb=" O ASP B 215 " pdb=" OG1 THR B 216 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 313 " pdb=" OG SER A 316 " model vdw 2.321 3.040 ... (remaining 113802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 256 or resid 264 through 294 or resid 297 throug \ h 555 or resid 564 through 642 or resid 677 through 896 or resid 1001 through 10 \ 04)) selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.470 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14171 Z= 0.240 Angle : 0.772 8.551 19211 Z= 0.430 Chirality : 0.052 0.371 2118 Planarity : 0.005 0.053 2475 Dihedral : 13.803 106.299 5582 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.19 % Allowed : 7.02 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.74 (0.20), residues: 1674 helix: -2.20 (0.33), residues: 183 sheet: -0.74 (0.27), residues: 350 loop : -1.13 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 402 HIS 0.009 0.001 HIS B 699 PHE 0.013 0.002 PHE B 790 TYR 0.018 0.002 TYR A 224 ARG 0.006 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 434 time to evaluate : 1.605 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: symmetry clash REVERT: A 248 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8387 (p0) REVERT: A 494 THR cc_start: 0.8827 (p) cc_final: 0.8609 (p) REVERT: A 617 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6850 (ttm-80) REVERT: A 642 LYS cc_start: 0.8972 (mttt) cc_final: 0.8696 (mmtt) REVERT: A 643 TYR cc_start: 0.7974 (p90) cc_final: 0.7352 (p90) REVERT: A 754 ASN cc_start: 0.7959 (m-40) cc_final: 0.7726 (p0) REVERT: A 820 LEU cc_start: 0.9264 (mt) cc_final: 0.8864 (mm) REVERT: A 822 TRP cc_start: 0.7541 (p90) cc_final: 0.7061 (p90) REVERT: A 848 GLU cc_start: 0.7887 (tp30) cc_final: 0.7683 (tp30) REVERT: A 850 VAL cc_start: 0.8481 (t) cc_final: 0.8218 (t) REVERT: A 893 TYR cc_start: 0.8067 (p90) cc_final: 0.7612 (p90) REVERT: B 83 TYR cc_start: 0.8573 (t80) cc_final: 0.8087 (t80) REVERT: B 92 MET cc_start: 0.8925 (mmm) cc_final: 0.8691 (mmm) REVERT: B 156 MET cc_start: 0.7631 (mmm) cc_final: 0.7151 (mtt) REVERT: B 174 ARG cc_start: 0.6762 (ptt90) cc_final: 0.5570 (ptt90) REVERT: B 214 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.3492 (t160) REVERT: B 350 LEU cc_start: 0.8641 (mt) cc_final: 0.8318 (mm) REVERT: B 352 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7329 (mm-30) REVERT: B 374 ASN cc_start: 0.8653 (m-40) cc_final: 0.8449 (m110) REVERT: B 388 TYR cc_start: 0.6573 (m-80) cc_final: 0.5875 (m-80) REVERT: B 415 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7727 (ptmt) REVERT: B 416 MET cc_start: 0.8437 (mtm) cc_final: 0.8013 (mtt) REVERT: B 477 ILE cc_start: 0.9394 (mt) cc_final: 0.9121 (mp) REVERT: B 572 LEU cc_start: 0.8670 (tp) cc_final: 0.8210 (tt) REVERT: B 612 SER cc_start: 0.8713 (m) cc_final: 0.8161 (p) REVERT: B 686 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 824 GLU cc_start: 0.8318 (tt0) cc_final: 0.8030 (tp30) REVERT: B 835 TYR cc_start: 0.8256 (m-80) cc_final: 0.7857 (m-80) REVERT: B 837 ILE cc_start: 0.8937 (mt) cc_final: 0.8700 (mt) outliers start: 33 outliers final: 12 residues processed: 457 average time/residue: 0.3113 time to fit residues: 196.0383 Evaluate side-chains 257 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 776 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 876 GLN B 399 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS B 696 ASN B 699 HIS ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14171 Z= 0.249 Angle : 0.747 8.099 19211 Z= 0.394 Chirality : 0.052 0.264 2118 Planarity : 0.005 0.056 2475 Dihedral : 9.826 69.573 2283 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.64 % Allowed : 12.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.60 (0.20), residues: 1674 helix: -1.77 (0.34), residues: 186 sheet: -0.62 (0.28), residues: 332 loop : -1.10 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.017 0.002 PHE B 90 TYR 0.027 0.002 TYR A 628 ARG 0.008 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.706 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: A 84 ASN cc_start: 0.8663 (m-40) cc_final: 0.8377 (t0) REVERT: A 373 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: A 477 ILE cc_start: 0.8973 (tt) cc_final: 0.8702 (mm) REVERT: A 494 THR cc_start: 0.8908 (p) cc_final: 0.8662 (p) REVERT: A 558 MET cc_start: 0.7684 (ttm) cc_final: 0.6840 (ttm) REVERT: A 586 ASP cc_start: 0.8704 (p0) cc_final: 0.8092 (p0) REVERT: A 602 ASN cc_start: 0.8938 (m-40) cc_final: 0.8633 (m-40) REVERT: A 617 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7078 (ttm170) REVERT: A 642 LYS cc_start: 0.8986 (mttt) cc_final: 0.8697 (mmtt) REVERT: A 643 TYR cc_start: 0.7847 (p90) cc_final: 0.7322 (p90) REVERT: A 704 VAL cc_start: 0.8708 (m) cc_final: 0.8473 (p) REVERT: A 754 ASN cc_start: 0.8050 (m-40) cc_final: 0.7730 (p0) REVERT: A 820 LEU cc_start: 0.9292 (mt) cc_final: 0.9023 (mm) REVERT: A 822 TRP cc_start: 0.7831 (p90) cc_final: 0.7230 (p90) REVERT: A 848 GLU cc_start: 0.7768 (tp30) cc_final: 0.7462 (tp30) REVERT: A 850 VAL cc_start: 0.8548 (t) cc_final: 0.8330 (t) REVERT: B 36 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8747 (mtmm) REVERT: B 79 TRP cc_start: 0.7770 (t60) cc_final: 0.7474 (t60) REVERT: B 156 MET cc_start: 0.7570 (mmm) cc_final: 0.7056 (mtp) REVERT: B 174 ARG cc_start: 0.6699 (ptt90) cc_final: 0.5337 (ptt90) REVERT: B 415 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7744 (ptmt) REVERT: B 416 MET cc_start: 0.8785 (mtm) cc_final: 0.8298 (mtp) REVERT: B 432 MET cc_start: 0.8610 (ttt) cc_final: 0.8387 (tpp) REVERT: B 469 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7834 (p) REVERT: B 476 ILE cc_start: 0.9054 (mt) cc_final: 0.8741 (mt) REVERT: B 572 LEU cc_start: 0.8761 (tp) cc_final: 0.8455 (tt) REVERT: B 686 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 751 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7511 (mtp180) REVERT: B 824 GLU cc_start: 0.8320 (tt0) cc_final: 0.8039 (tp30) REVERT: B 835 TYR cc_start: 0.8145 (m-80) cc_final: 0.7404 (m-80) REVERT: B 857 LYS cc_start: 0.9430 (tttt) cc_final: 0.9141 (ttmm) outliers start: 55 outliers final: 25 residues processed: 294 average time/residue: 0.2884 time to fit residues: 121.3416 Evaluate side-chains 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 563 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN B 846 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14171 Z= 0.188 Angle : 0.682 9.670 19211 Z= 0.356 Chirality : 0.049 0.246 2118 Planarity : 0.004 0.047 2475 Dihedral : 8.812 61.079 2269 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 3.31 % Allowed : 14.50 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.54 (0.20), residues: 1674 helix: -1.56 (0.36), residues: 182 sheet: -0.57 (0.27), residues: 334 loop : -1.10 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 404 HIS 0.010 0.001 HIS B 699 PHE 0.017 0.001 PHE C 61 TYR 0.018 0.002 TYR C 25 ARG 0.010 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 1.658 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: A 84 ASN cc_start: 0.8622 (m-40) cc_final: 0.8328 (t0) REVERT: A 277 CYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6439 (m) REVERT: A 319 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7917 (ptm) REVERT: A 373 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8110 (mtmm) REVERT: A 461 ASP cc_start: 0.7900 (m-30) cc_final: 0.7670 (m-30) REVERT: A 494 THR cc_start: 0.8844 (p) cc_final: 0.8621 (p) REVERT: A 586 ASP cc_start: 0.8671 (p0) cc_final: 0.8062 (p0) REVERT: A 602 ASN cc_start: 0.8905 (m-40) cc_final: 0.8634 (m-40) REVERT: A 617 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7102 (ttm170) REVERT: A 642 LYS cc_start: 0.8958 (mttt) cc_final: 0.8688 (mmtt) REVERT: A 643 TYR cc_start: 0.7820 (p90) cc_final: 0.7326 (p90) REVERT: A 704 VAL cc_start: 0.8702 (m) cc_final: 0.8487 (p) REVERT: A 820 LEU cc_start: 0.9290 (mt) cc_final: 0.9035 (mm) REVERT: A 833 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8349 (pt) REVERT: A 848 GLU cc_start: 0.7838 (tp30) cc_final: 0.7572 (tp30) REVERT: B 156 MET cc_start: 0.7566 (mmm) cc_final: 0.7032 (mtt) REVERT: B 174 ARG cc_start: 0.6535 (ptt90) cc_final: 0.5390 (ptt90) REVERT: B 270 ASP cc_start: 0.7681 (t0) cc_final: 0.7436 (t0) REVERT: B 309 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8213 (tttm) REVERT: B 389 SER cc_start: 0.8911 (t) cc_final: 0.8669 (p) REVERT: B 477 ILE cc_start: 0.9408 (mt) cc_final: 0.9167 (mp) REVERT: B 572 LEU cc_start: 0.8780 (tp) cc_final: 0.8398 (tt) REVERT: B 686 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 835 TYR cc_start: 0.8142 (m-80) cc_final: 0.7530 (m-80) REVERT: B 855 TYR cc_start: 0.7920 (t80) cc_final: 0.7173 (t80) REVERT: B 857 LYS cc_start: 0.9414 (tttt) cc_final: 0.9146 (ttmm) REVERT: B 885 SER cc_start: 0.9168 (t) cc_final: 0.8913 (p) outliers start: 50 outliers final: 24 residues processed: 263 average time/residue: 0.2815 time to fit residues: 106.7616 Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS B 338 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 14171 Z= 0.371 Angle : 0.738 9.522 19211 Z= 0.385 Chirality : 0.051 0.274 2118 Planarity : 0.005 0.043 2475 Dihedral : 8.465 59.927 2265 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 4.04 % Allowed : 15.83 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.53 (0.20), residues: 1674 helix: -1.61 (0.35), residues: 183 sheet: -0.54 (0.28), residues: 329 loop : -1.09 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 618 HIS 0.018 0.002 HIS A 563 PHE 0.020 0.002 PHE C 61 TYR 0.023 0.002 TYR A 391 ARG 0.009 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 1.730 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: A 91 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7492 (mp0) REVERT: A 319 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: A 373 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: A 461 ASP cc_start: 0.8019 (m-30) cc_final: 0.7723 (m-30) REVERT: A 494 THR cc_start: 0.8923 (p) cc_final: 0.8721 (p) REVERT: A 586 ASP cc_start: 0.8769 (p0) cc_final: 0.8281 (p0) REVERT: A 602 ASN cc_start: 0.9030 (m-40) cc_final: 0.8704 (m-40) REVERT: A 617 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7112 (ttm170) REVERT: A 642 LYS cc_start: 0.9013 (mttt) cc_final: 0.8804 (mmtt) REVERT: A 643 TYR cc_start: 0.7922 (p90) cc_final: 0.7398 (p90) REVERT: A 704 VAL cc_start: 0.8825 (m) cc_final: 0.8570 (p) REVERT: A 754 ASN cc_start: 0.8243 (m-40) cc_final: 0.7846 (p0) REVERT: A 846 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8279 (mt0) REVERT: A 848 GLU cc_start: 0.8065 (tp30) cc_final: 0.7636 (tp30) REVERT: B 156 MET cc_start: 0.7677 (mmm) cc_final: 0.7202 (mmp) REVERT: B 270 ASP cc_start: 0.7834 (t0) cc_final: 0.7532 (t0) REVERT: B 389 SER cc_start: 0.8984 (t) cc_final: 0.8631 (p) REVERT: B 416 MET cc_start: 0.8373 (mtp) cc_final: 0.8152 (mtt) REVERT: B 686 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 751 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7580 (mtp180) REVERT: B 857 LYS cc_start: 0.9436 (tttt) cc_final: 0.9166 (ttmm) outliers start: 61 outliers final: 31 residues processed: 247 average time/residue: 0.3112 time to fit residues: 111.4115 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14171 Z= 0.265 Angle : 0.684 11.014 19211 Z= 0.355 Chirality : 0.049 0.261 2118 Planarity : 0.004 0.064 2475 Dihedral : 8.184 59.244 2264 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 3.18 % Allowed : 17.68 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.47 (0.20), residues: 1674 helix: -1.43 (0.36), residues: 183 sheet: -0.43 (0.29), residues: 313 loop : -1.09 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.016 0.001 PHE C 61 TYR 0.027 0.002 TYR A 835 ARG 0.010 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.637 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 319 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8028 (ttp) REVERT: A 373 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8201 (mtmm) REVERT: A 430 TYR cc_start: 0.8506 (m-80) cc_final: 0.8254 (m-10) REVERT: A 461 ASP cc_start: 0.7953 (m-30) cc_final: 0.7750 (m-30) REVERT: A 494 THR cc_start: 0.8953 (p) cc_final: 0.8740 (p) REVERT: A 586 ASP cc_start: 0.8778 (p0) cc_final: 0.8324 (p0) REVERT: A 602 ASN cc_start: 0.9022 (m-40) cc_final: 0.8680 (m-40) REVERT: A 643 TYR cc_start: 0.7954 (p90) cc_final: 0.7427 (p90) REVERT: A 848 GLU cc_start: 0.8226 (tp30) cc_final: 0.7760 (tp30) REVERT: A 857 LYS cc_start: 0.8896 (mttp) cc_final: 0.8682 (mttp) REVERT: B 39 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7613 (t70) REVERT: B 156 MET cc_start: 0.7572 (mmm) cc_final: 0.7081 (mmp) REVERT: B 174 ARG cc_start: 0.6592 (ptt90) cc_final: 0.6010 (ptt90) REVERT: B 270 ASP cc_start: 0.7879 (t0) cc_final: 0.7524 (t0) REVERT: B 336 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7831 (ttp-170) REVERT: B 389 SER cc_start: 0.9001 (t) cc_final: 0.8590 (p) REVERT: B 686 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 751 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7511 (mtp180) REVERT: B 835 TYR cc_start: 0.8073 (m-80) cc_final: 0.7528 (m-80) REVERT: B 857 LYS cc_start: 0.9425 (tttt) cc_final: 0.9185 (ttmm) outliers start: 48 outliers final: 35 residues processed: 240 average time/residue: 0.2753 time to fit residues: 95.8154 Evaluate side-chains 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14171 Z= 0.228 Angle : 0.669 8.864 19211 Z= 0.345 Chirality : 0.049 0.253 2118 Planarity : 0.004 0.050 2475 Dihedral : 7.947 59.697 2260 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.12 % Favored : 91.82 % Rotamer: Outliers : 3.44 % Allowed : 17.68 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.41 (0.20), residues: 1674 helix: -1.16 (0.38), residues: 175 sheet: -0.48 (0.29), residues: 320 loop : -1.06 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.021 0.001 PHE C 61 TYR 0.017 0.002 TYR A 391 ARG 0.008 0.001 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 1.694 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: A 319 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8066 (ttp) REVERT: A 373 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8212 (mtmm) REVERT: A 412 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8356 (tptp) REVERT: A 430 TYR cc_start: 0.8478 (m-80) cc_final: 0.8267 (m-10) REVERT: A 461 ASP cc_start: 0.8031 (m-30) cc_final: 0.7707 (m-30) REVERT: A 494 THR cc_start: 0.8969 (p) cc_final: 0.8747 (p) REVERT: A 586 ASP cc_start: 0.8783 (p0) cc_final: 0.8371 (p0) REVERT: A 602 ASN cc_start: 0.8997 (m-40) cc_final: 0.8637 (m-40) REVERT: A 643 TYR cc_start: 0.7957 (p90) cc_final: 0.7435 (p90) REVERT: A 822 TRP cc_start: 0.8187 (p90) cc_final: 0.7510 (p90) REVERT: A 847 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8215 (mmm-85) REVERT: A 848 GLU cc_start: 0.8261 (tp30) cc_final: 0.7624 (tp30) REVERT: B 39 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (t70) REVERT: B 81 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 156 MET cc_start: 0.7552 (mmm) cc_final: 0.7049 (mmp) REVERT: B 270 ASP cc_start: 0.7926 (t0) cc_final: 0.7563 (t0) REVERT: B 336 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7962 (ttp-170) REVERT: B 389 SER cc_start: 0.8987 (t) cc_final: 0.8581 (p) REVERT: B 686 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 835 TYR cc_start: 0.8076 (m-80) cc_final: 0.7594 (m-80) REVERT: B 857 LYS cc_start: 0.9415 (tttt) cc_final: 0.9171 (ttmm) outliers start: 52 outliers final: 34 residues processed: 237 average time/residue: 0.2583 time to fit residues: 90.3082 Evaluate side-chains 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14171 Z= 0.272 Angle : 0.678 12.093 19211 Z= 0.349 Chirality : 0.049 0.248 2118 Planarity : 0.004 0.041 2475 Dihedral : 7.803 58.343 2260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 3.25 % Allowed : 18.28 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.31 (0.20), residues: 1674 helix: -0.66 (0.41), residues: 164 sheet: -0.51 (0.29), residues: 318 loop : -1.04 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.024 0.002 PHE C 61 TYR 0.019 0.002 TYR A 391 ARG 0.008 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.859 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 319 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8165 (ttp) REVERT: A 373 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: A 430 TYR cc_start: 0.8593 (m-80) cc_final: 0.8347 (m-10) REVERT: A 461 ASP cc_start: 0.8069 (m-30) cc_final: 0.7721 (m-30) REVERT: A 494 THR cc_start: 0.9037 (p) cc_final: 0.8822 (p) REVERT: A 586 ASP cc_start: 0.8790 (p0) cc_final: 0.8422 (p0) REVERT: A 602 ASN cc_start: 0.9054 (m-40) cc_final: 0.8701 (m-40) REVERT: A 643 TYR cc_start: 0.7967 (p90) cc_final: 0.7421 (p90) REVERT: A 687 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: A 822 TRP cc_start: 0.8272 (p90) cc_final: 0.7548 (p90) REVERT: A 848 GLU cc_start: 0.8359 (tp30) cc_final: 0.7702 (tp30) REVERT: B 39 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7662 (t70) REVERT: B 81 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 156 MET cc_start: 0.7542 (mmm) cc_final: 0.7271 (mmt) REVERT: B 242 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7621 (mt-10) REVERT: B 270 ASP cc_start: 0.8057 (t0) cc_final: 0.7722 (t0) REVERT: B 336 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8022 (ttp-170) REVERT: B 343 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8522 (mp0) REVERT: B 389 SER cc_start: 0.9009 (t) cc_final: 0.8582 (p) REVERT: B 415 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7967 (ttpt) REVERT: B 686 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 751 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7533 (mtp180) REVERT: B 835 TYR cc_start: 0.8048 (m-80) cc_final: 0.7696 (m-80) outliers start: 49 outliers final: 31 residues processed: 230 average time/residue: 0.2629 time to fit residues: 89.3451 Evaluate side-chains 218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 chunk 148 optimal weight: 0.0670 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14171 Z= 0.231 Angle : 0.667 14.150 19211 Z= 0.341 Chirality : 0.048 0.247 2118 Planarity : 0.004 0.041 2475 Dihedral : 7.587 58.211 2258 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 3.18 % Allowed : 18.74 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1674 helix: -0.59 (0.41), residues: 163 sheet: -0.50 (0.29), residues: 326 loop : -1.03 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.023 0.001 PHE C 61 TYR 0.017 0.002 TYR A 391 ARG 0.009 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.836 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: A 240 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7789 (mtm110) REVERT: A 319 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: A 373 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8176 (mtmm) REVERT: A 430 TYR cc_start: 0.8678 (m-80) cc_final: 0.8403 (m-10) REVERT: A 461 ASP cc_start: 0.8098 (m-30) cc_final: 0.7696 (m-30) REVERT: A 494 THR cc_start: 0.9045 (p) cc_final: 0.8837 (p) REVERT: A 586 ASP cc_start: 0.8784 (p0) cc_final: 0.8416 (p0) REVERT: A 602 ASN cc_start: 0.9031 (m-40) cc_final: 0.8679 (m-40) REVERT: A 643 TYR cc_start: 0.7934 (p90) cc_final: 0.7677 (p90) REVERT: A 704 VAL cc_start: 0.8652 (m) cc_final: 0.8429 (p) REVERT: A 754 ASN cc_start: 0.8218 (m-40) cc_final: 0.7820 (p0) REVERT: A 822 TRP cc_start: 0.8245 (p90) cc_final: 0.7087 (p90) REVERT: A 848 GLU cc_start: 0.8384 (tp30) cc_final: 0.7917 (tp30) REVERT: B 39 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (t70) REVERT: B 156 MET cc_start: 0.7550 (mmm) cc_final: 0.7253 (mmp) REVERT: B 184 MET cc_start: 0.5423 (tmm) cc_final: 0.5191 (tmm) REVERT: B 270 ASP cc_start: 0.8161 (t0) cc_final: 0.7892 (t0) REVERT: B 336 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8071 (ttp-170) REVERT: B 389 SER cc_start: 0.9003 (t) cc_final: 0.8572 (p) REVERT: B 506 THR cc_start: 0.8871 (p) cc_final: 0.8666 (t) REVERT: B 686 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 751 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7481 (mtp180) outliers start: 48 outliers final: 35 residues processed: 229 average time/residue: 0.2632 time to fit residues: 89.6484 Evaluate side-chains 223 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14171 Z= 0.219 Angle : 0.668 14.979 19211 Z= 0.340 Chirality : 0.048 0.246 2118 Planarity : 0.004 0.040 2475 Dihedral : 7.424 58.337 2258 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.53 % Favored : 92.35 % Rotamer: Outliers : 2.65 % Allowed : 19.67 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.27 (0.20), residues: 1674 helix: -0.56 (0.42), residues: 164 sheet: -0.45 (0.29), residues: 312 loop : -1.03 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.021 0.001 PHE C 61 TYR 0.020 0.002 TYR B 835 ARG 0.009 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.729 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: A 373 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8203 (mtmm) REVERT: A 430 TYR cc_start: 0.8686 (m-80) cc_final: 0.8421 (m-10) REVERT: A 432 MET cc_start: 0.7775 (tpp) cc_final: 0.7574 (mmm) REVERT: A 461 ASP cc_start: 0.8127 (m-30) cc_final: 0.7717 (m-30) REVERT: A 586 ASP cc_start: 0.8739 (p0) cc_final: 0.8371 (p0) REVERT: A 602 ASN cc_start: 0.9012 (m-40) cc_final: 0.8663 (m-40) REVERT: A 643 TYR cc_start: 0.7927 (p90) cc_final: 0.7687 (p90) REVERT: A 704 VAL cc_start: 0.8636 (m) cc_final: 0.8420 (p) REVERT: A 754 ASN cc_start: 0.8177 (m-40) cc_final: 0.7799 (p0) REVERT: A 822 TRP cc_start: 0.8218 (p90) cc_final: 0.7197 (p90) REVERT: A 848 GLU cc_start: 0.8383 (tp30) cc_final: 0.7701 (tp30) REVERT: B 39 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7576 (t0) REVERT: B 156 MET cc_start: 0.7541 (mmm) cc_final: 0.7244 (mmp) REVERT: B 336 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8045 (ttp-170) REVERT: B 343 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8529 (mp0) REVERT: B 389 SER cc_start: 0.9036 (t) cc_final: 0.8568 (p) REVERT: B 506 THR cc_start: 0.8875 (p) cc_final: 0.8660 (t) REVERT: B 686 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 834 MET cc_start: 0.7161 (ppp) cc_final: 0.6957 (ttt) REVERT: B 878 THR cc_start: 0.9156 (m) cc_final: 0.8785 (p) outliers start: 40 outliers final: 32 residues processed: 223 average time/residue: 0.2619 time to fit residues: 87.7317 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 62 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 154 optimal weight: 0.0040 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 339 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14171 Z= 0.233 Angle : 0.679 13.500 19211 Z= 0.346 Chirality : 0.048 0.242 2118 Planarity : 0.005 0.041 2475 Dihedral : 7.345 58.219 2258 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.29 % Rotamer: Outliers : 2.52 % Allowed : 20.07 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.31 (0.20), residues: 1674 helix: -0.68 (0.41), residues: 170 sheet: -0.45 (0.29), residues: 318 loop : -1.06 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.021 0.001 PHE C 61 TYR 0.018 0.002 TYR B 835 ARG 0.010 0.001 ARG B 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.688 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: A 240 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7271 (mtm-85) REVERT: A 373 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8197 (mtmm) REVERT: A 430 TYR cc_start: 0.8691 (m-80) cc_final: 0.8428 (m-10) REVERT: A 432 MET cc_start: 0.7835 (tpp) cc_final: 0.7609 (mmm) REVERT: A 461 ASP cc_start: 0.8023 (m-30) cc_final: 0.7643 (m-30) REVERT: A 586 ASP cc_start: 0.8740 (p0) cc_final: 0.8400 (p0) REVERT: A 602 ASN cc_start: 0.9016 (m-40) cc_final: 0.8680 (m-40) REVERT: A 643 TYR cc_start: 0.7887 (p90) cc_final: 0.7638 (p90) REVERT: A 704 VAL cc_start: 0.8680 (m) cc_final: 0.8472 (p) REVERT: A 754 ASN cc_start: 0.8168 (m-40) cc_final: 0.7792 (p0) REVERT: A 822 TRP cc_start: 0.8239 (p90) cc_final: 0.7237 (p90) REVERT: A 848 GLU cc_start: 0.8401 (tp30) cc_final: 0.7910 (tp30) REVERT: B 39 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7594 (t0) REVERT: B 156 MET cc_start: 0.7535 (mmm) cc_final: 0.7236 (mmp) REVERT: B 184 MET cc_start: 0.7288 (mmm) cc_final: 0.6824 (tmm) REVERT: B 336 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7872 (ttp-170) REVERT: B 343 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8531 (mp0) REVERT: B 389 SER cc_start: 0.9038 (t) cc_final: 0.8516 (p) REVERT: B 506 THR cc_start: 0.8884 (p) cc_final: 0.8676 (t) REVERT: B 686 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8239 (mt-10) REVERT: B 751 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7641 (mtp180) REVERT: B 878 THR cc_start: 0.9158 (m) cc_final: 0.8816 (p) outliers start: 38 outliers final: 33 residues processed: 216 average time/residue: 0.2657 time to fit residues: 84.9536 Evaluate side-chains 218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 62 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.124878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099668 restraints weight = 30433.619| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.72 r_work: 0.3506 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14171 Z= 0.198 Angle : 0.656 11.752 19211 Z= 0.335 Chirality : 0.048 0.241 2118 Planarity : 0.004 0.040 2475 Dihedral : 7.178 58.388 2258 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.23 % Favored : 92.65 % Rotamer: Outliers : 2.32 % Allowed : 20.07 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.31 (0.20), residues: 1674 helix: -0.68 (0.41), residues: 171 sheet: -0.42 (0.29), residues: 316 loop : -1.07 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.017 0.001 PHE C 61 TYR 0.017 0.001 TYR A 893 ARG 0.010 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.87 seconds wall clock time: 62 minutes 49.02 seconds (3769.02 seconds total)