Starting phenix.real_space_refine on Wed Feb 21 06:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bcj_7081/02_2024/6bcj_7081.pdb" } resolution = 3.14 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= 0.010 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Na 4 4.78 5 C 19260 2.51 5 N 5216 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 888": "NH1" <-> "NH2" Residue "B ARG 949": "NH1" <-> "NH2" Residue "B ARG 953": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 993": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1118": "NH1" <-> "NH2" Residue "B ARG 1137": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 949": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1063": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 878": "NH1" <-> "NH2" Residue "C ARG 888": "NH1" <-> "NH2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C ARG 953": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 993": "NH1" <-> "NH2" Residue "C ARG 1063": "NH1" <-> "NH2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C ARG 1137": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 888": "NH1" <-> "NH2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 953": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 993": "NH1" <-> "NH2" Residue "D ARG 1063": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1137": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29868 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "C" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "D" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7464 Classifications: {'peptide': 936} Link IDs: {'PTRANS': 37, 'TRANS': 898} Chain breaks: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 15.41, per 1000 atoms: 0.52 Number of scatterers: 29868 At special positions: 0 Unit cell: (150.87, 150.87, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 Na 4 11.00 O 5252 8.00 N 5216 7.00 C 19260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.65 Conformation dependent library (CDL) restraints added in 5.3 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 12 sheets defined 68.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.544A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.783A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 416 removed outlier: 4.246A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 668' Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 704' Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 Processing helix chain 'B' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP B 858 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.815A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 966 - end of helix Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.967A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1162 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.720A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.613A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.564A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.570A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 Processing helix chain 'A' and resid 849 through 858 removed outlier: 3.889A pdb=" N ASP A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 920 removed outlier: 4.649A pdb=" N LYS A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1162 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.992A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.705A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.622A pdb=" N GLN C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.749A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 358 removed outlier: 3.543A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 362 removed outlier: 3.762A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.691A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 4.113A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.839A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 704' Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 Processing helix chain 'C' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 3.538A pdb=" N GLY C 887 " --> pdb=" O LEU C 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG C 965 " --> pdb=" O ARG C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1162 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.991A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.706A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.969A pdb=" N MET D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 202 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.623A pdb=" N GLN D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.750A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 5.100A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.545A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 362 removed outlier: 3.763A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.782A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.245A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.637A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.692A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.721A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.112A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.615A pdb=" N VAL D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.612A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.565A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.838A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 668' Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 704 removed outlier: 3.571A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 704' Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 Processing helix chain 'D' and resid 849 through 858 removed outlier: 3.890A pdb=" N ASP D 858 " --> pdb=" O LEU D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.908A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 3.537A pdb=" N GLY D 887 " --> pdb=" O LEU D 883 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 removed outlier: 3.654A pdb=" N PHE D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 920 removed outlier: 4.648A pdb=" N LYS D 915 " --> pdb=" O GLN D 911 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.816A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 970 removed outlier: 5.190A pdb=" N ARG D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Proline residue: D 966 - end of helix Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.968A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.785A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D1056 " --> pdb=" O LEU D1052 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1162 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 211 removed outlier: 6.835A pdb=" N ALA B 210 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP B 78 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 92 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 119 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 277 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER B 121 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 302 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 987 removed outlier: 3.947A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 987 " --> pdb=" O TRP B 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP B 996 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.833A pdb=" N ALA A 210 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP A 78 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 92 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 119 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 277 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER A 121 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 302 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 987 " --> pdb=" O TRP A 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP A 996 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA C 210 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP C 78 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 92 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 119 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 277 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER C 121 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 302 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.948A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 987 " --> pdb=" O TRP C 996 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP C 996 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 211 removed outlier: 6.834A pdb=" N ALA D 210 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP D 78 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 92 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL D 119 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU D 277 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER D 121 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 302 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 987 removed outlier: 3.946A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 987 " --> pdb=" O TRP D 996 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP D 996 " --> pdb=" O GLY D 987 " (cutoff:3.500A) 1698 hydrogen bonds defined for protein. 5034 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: 10.34 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8037 1.33 - 1.46: 6828 1.46 - 1.58: 15459 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 30528 Sorted by residual: bond pdb=" CB VAL C 776 " pdb=" CG1 VAL C 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" CB VAL A 776 " pdb=" CG1 VAL A 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.42e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" C PHE A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.36e+00 bond pdb=" CB VAL B 776 " pdb=" CG1 VAL B 776 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 30523 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.46: 569 105.46 - 112.62: 15874 112.62 - 119.78: 10630 119.78 - 126.94: 13846 126.94 - 134.09: 453 Bond angle restraints: 41372 Sorted by residual: angle pdb=" N PRO B1073 " pdb=" CA PRO B1073 " pdb=" C PRO B1073 " ideal model delta sigma weight residual 110.70 117.10 -6.40 1.22e+00 6.72e-01 2.75e+01 angle pdb=" N PRO D1073 " pdb=" CA PRO D1073 " pdb=" C PRO D1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO A1073 " pdb=" CA PRO A1073 " pdb=" C PRO A1073 " ideal model delta sigma weight residual 110.70 117.08 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N PRO C1073 " pdb=" CA PRO C1073 " pdb=" C PRO C1073 " ideal model delta sigma weight residual 110.70 117.05 -6.35 1.22e+00 6.72e-01 2.71e+01 angle pdb=" CB ARG C 965 " pdb=" CG ARG C 965 " pdb=" CD ARG C 965 " ideal model delta sigma weight residual 111.30 100.48 10.82 2.30e+00 1.89e-01 2.21e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 17373 16.49 - 32.98: 619 32.98 - 49.46: 96 49.46 - 65.95: 8 65.95 - 82.44: 20 Dihedral angle restraints: 18116 sinusoidal: 7320 harmonic: 10796 Sorted by residual: dihedral pdb=" CB CYS B 989 " pdb=" SG CYS B 989 " pdb=" SG CYS B1007 " pdb=" CB CYS B1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.43 82.43 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2983 0.048 - 0.096: 1377 0.096 - 0.143: 273 0.143 - 0.191: 39 0.191 - 0.239: 4 Chirality restraints: 4676 Sorted by residual: chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4673 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.030 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP B 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.030 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 816 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 816 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.008 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8780 2.82 - 3.34: 26099 3.34 - 3.86: 46204 3.86 - 4.38: 53211 4.38 - 4.90: 93129 Nonbonded interactions: 227423 Sorted by model distance: nonbonded pdb=" O LEU D 948 " pdb=" CD1 LEU D 948 " model vdw 2.301 3.460 nonbonded pdb=" O LEU B 948 " pdb=" CD1 LEU B 948 " model vdw 2.303 3.460 nonbonded pdb=" O LEU A 948 " pdb=" CD1 LEU A 948 " model vdw 2.306 3.460 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.331 2.440 nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.332 2.440 ... (remaining 227418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 1162) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.660 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 74.860 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.008 0.070 30528 Z= 0.527 Angle : 0.968 10.821 41372 Z= 0.531 Chirality : 0.053 0.239 4676 Planarity : 0.007 0.071 5208 Dihedral : 9.603 77.213 11112 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.09), residues: 3672 helix: -3.23 (0.06), residues: 2348 sheet: -1.40 (0.29), residues: 216 loop : -3.00 (0.15), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 816 HIS 0.008 0.002 HIS B 166 PHE 0.035 0.004 PHE D 81 TYR 0.021 0.003 TYR A 339 ARG 0.009 0.001 ARG D1058 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 566 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 LEU cc_start: 0.8106 (tp) cc_final: 0.7878 (mt) REVERT: B 252 LEU cc_start: 0.7854 (tp) cc_final: 0.7441 (tp) REVERT: B 454 HIS cc_start: 0.7438 (t70) cc_final: 0.7153 (t-90) REVERT: B 849 ARG cc_start: 0.5820 (mtt180) cc_final: 0.4987 (ptm160) REVERT: B 1140 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7772 (ttp-110) REVERT: B 1143 ASP cc_start: 0.8159 (m-30) cc_final: 0.7924 (m-30) REVERT: A 94 LEU cc_start: 0.8219 (tp) cc_final: 0.7985 (mt) REVERT: A 169 VAL cc_start: 0.7636 (t) cc_final: 0.7397 (m) REVERT: A 252 LEU cc_start: 0.7942 (tp) cc_final: 0.7513 (tp) REVERT: A 454 HIS cc_start: 0.7377 (t70) cc_final: 0.7064 (t-90) REVERT: A 849 ARG cc_start: 0.5881 (mtt180) cc_final: 0.5047 (ptm160) REVERT: A 1140 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7824 (ttp-110) REVERT: A 1141 ASP cc_start: 0.8018 (m-30) cc_final: 0.7727 (m-30) REVERT: A 1143 ASP cc_start: 0.8157 (m-30) cc_final: 0.7905 (m-30) REVERT: C 94 LEU cc_start: 0.8140 (tp) cc_final: 0.7919 (mt) REVERT: C 411 GLN cc_start: 0.8141 (tt0) cc_final: 0.7912 (tp40) REVERT: C 454 HIS cc_start: 0.7485 (t70) cc_final: 0.7192 (t-90) REVERT: C 849 ARG cc_start: 0.5760 (mtt180) cc_final: 0.4934 (ptm160) REVERT: C 1140 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7823 (ttp-110) REVERT: C 1141 ASP cc_start: 0.7982 (m-30) cc_final: 0.7681 (m-30) REVERT: C 1143 ASP cc_start: 0.8159 (m-30) cc_final: 0.7908 (m-30) REVERT: D 94 LEU cc_start: 0.8104 (tp) cc_final: 0.7894 (mt) REVERT: D 411 GLN cc_start: 0.8162 (tt0) cc_final: 0.7925 (tp40) REVERT: D 454 HIS cc_start: 0.7486 (t70) cc_final: 0.7206 (t-90) REVERT: D 849 ARG cc_start: 0.5783 (mtt180) cc_final: 0.4960 (ptm160) REVERT: D 1141 ASP cc_start: 0.7993 (m-30) cc_final: 0.7689 (m-30) REVERT: D 1143 ASP cc_start: 0.8165 (m-30) cc_final: 0.7912 (m-30) outliers start: 12 outliers final: 0 residues processed: 578 average time/residue: 0.4984 time to fit residues: 425.6361 Evaluate side-chains 301 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN B 782 ASN B1010 GLN B1013 ASN B1080 HIS A 261 GLN A 782 ASN A1010 GLN A1013 ASN A1080 HIS C 261 GLN C 782 ASN C1010 GLN C1013 ASN C1080 HIS D 261 GLN D 782 ASN D1010 GLN D1013 ASN D1080 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 30528 Z= 0.172 Angle : 0.556 10.682 41372 Z= 0.288 Chirality : 0.037 0.161 4676 Planarity : 0.005 0.052 5208 Dihedral : 4.542 21.566 4092 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.16 % Allowed : 7.38 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 3672 helix: -0.27 (0.10), residues: 2384 sheet: -1.16 (0.30), residues: 216 loop : -2.60 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 214 HIS 0.004 0.001 HIS C 166 PHE 0.018 0.002 PHE B 793 TYR 0.016 0.001 TYR C 964 ARG 0.007 0.000 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 390 time to evaluate : 3.673 Fit side-chains REVERT: B 241 TYR cc_start: 0.6869 (m-80) cc_final: 0.6526 (m-80) REVERT: B 278 LEU cc_start: 0.7337 (tp) cc_final: 0.7132 (tt) REVERT: B 454 HIS cc_start: 0.7306 (t70) cc_final: 0.6933 (t-90) REVERT: B 849 ARG cc_start: 0.5530 (mtt180) cc_final: 0.4798 (ptm160) REVERT: A 224 PHE cc_start: 0.7998 (m-80) cc_final: 0.7682 (m-80) REVERT: A 454 HIS cc_start: 0.7294 (t70) cc_final: 0.6938 (t-90) REVERT: A 614 ASP cc_start: 0.7821 (t70) cc_final: 0.7606 (t0) REVERT: A 849 ARG cc_start: 0.5471 (mtt180) cc_final: 0.4792 (ptm160) REVERT: C 224 PHE cc_start: 0.7868 (m-80) cc_final: 0.7522 (m-80) REVERT: C 252 LEU cc_start: 0.7599 (tp) cc_final: 0.7191 (mp) REVERT: C 411 GLN cc_start: 0.7873 (tt0) cc_final: 0.7625 (tp40) REVERT: C 454 HIS cc_start: 0.7369 (t70) cc_final: 0.6955 (t-90) REVERT: C 849 ARG cc_start: 0.5462 (mtt180) cc_final: 0.4751 (ptm160) REVERT: D 224 PHE cc_start: 0.7827 (m-80) cc_final: 0.7466 (m-80) REVERT: D 241 TYR cc_start: 0.6781 (m-80) cc_final: 0.6446 (m-80) REVERT: D 252 LEU cc_start: 0.7606 (tp) cc_final: 0.7211 (mp) REVERT: D 411 GLN cc_start: 0.7889 (tt0) cc_final: 0.7468 (tp-100) REVERT: D 454 HIS cc_start: 0.7371 (t70) cc_final: 0.6964 (t-90) REVERT: D 614 ASP cc_start: 0.7827 (t70) cc_final: 0.7586 (t0) REVERT: D 849 ARG cc_start: 0.5405 (mtt180) cc_final: 0.4703 (ptm160) outliers start: 37 outliers final: 23 residues processed: 415 average time/residue: 0.4797 time to fit residues: 300.0064 Evaluate side-chains 309 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 1013 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 0.8980 chunk 365 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 454 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 30528 Z= 0.339 Angle : 0.631 11.063 41372 Z= 0.323 Chirality : 0.041 0.185 4676 Planarity : 0.005 0.045 5208 Dihedral : 4.451 19.704 4092 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.72 % Allowed : 8.53 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3672 helix: 0.78 (0.10), residues: 2368 sheet: -0.86 (0.31), residues: 208 loop : -2.58 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 816 HIS 0.004 0.001 HIS D 853 PHE 0.033 0.002 PHE B 906 TYR 0.015 0.002 TYR B 339 ARG 0.010 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 271 time to evaluate : 3.159 Fit side-chains REVERT: B 224 PHE cc_start: 0.8022 (m-80) cc_final: 0.7731 (m-80) REVERT: B 241 TYR cc_start: 0.6753 (m-80) cc_final: 0.6535 (m-80) REVERT: B 252 LEU cc_start: 0.7478 (tt) cc_final: 0.7212 (tp) REVERT: B 278 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7065 (tt) REVERT: B 454 HIS cc_start: 0.7349 (t-90) cc_final: 0.6927 (t-90) REVERT: B 699 CYS cc_start: 0.7562 (t) cc_final: 0.7300 (t) REVERT: B 849 ARG cc_start: 0.5450 (mtt180) cc_final: 0.4778 (ptm160) REVERT: B 937 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 948 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (pp) REVERT: B 1141 ASP cc_start: 0.8027 (t0) cc_final: 0.7561 (t0) REVERT: A 169 VAL cc_start: 0.7511 (t) cc_final: 0.7186 (m) REVERT: A 224 PHE cc_start: 0.8023 (m-80) cc_final: 0.7749 (m-80) REVERT: A 241 TYR cc_start: 0.7035 (m-80) cc_final: 0.6827 (m-80) REVERT: A 252 LEU cc_start: 0.7587 (tt) cc_final: 0.7314 (tp) REVERT: A 454 HIS cc_start: 0.7291 (t-90) cc_final: 0.6920 (t-90) REVERT: A 574 MET cc_start: 0.8713 (mmm) cc_final: 0.8433 (mtt) REVERT: A 849 ARG cc_start: 0.5434 (mtt180) cc_final: 0.4779 (ptm160) REVERT: A 937 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 948 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8650 (pp) REVERT: A 1141 ASP cc_start: 0.7749 (t0) cc_final: 0.7498 (t0) REVERT: C 224 PHE cc_start: 0.7962 (m-80) cc_final: 0.7656 (m-80) REVERT: C 252 LEU cc_start: 0.7636 (tp) cc_final: 0.7217 (mp) REVERT: C 285 MET cc_start: 0.5719 (mmp) cc_final: 0.5003 (mmt) REVERT: C 288 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6769 (mtm180) REVERT: C 454 HIS cc_start: 0.7377 (t-90) cc_final: 0.7070 (t-90) REVERT: C 574 MET cc_start: 0.8721 (mmm) cc_final: 0.8448 (mtt) REVERT: C 699 CYS cc_start: 0.7620 (t) cc_final: 0.7323 (t) REVERT: C 849 ARG cc_start: 0.5410 (mtt180) cc_final: 0.4735 (ptm160) REVERT: C 851 ARG cc_start: 0.4717 (mtt180) cc_final: 0.4265 (mtp85) REVERT: C 937 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 1141 ASP cc_start: 0.7763 (t0) cc_final: 0.7509 (t0) REVERT: D 224 PHE cc_start: 0.7974 (m-80) cc_final: 0.7653 (m-80) REVERT: D 241 TYR cc_start: 0.6720 (m-80) cc_final: 0.6515 (m-80) REVERT: D 252 LEU cc_start: 0.7613 (tp) cc_final: 0.7201 (mp) REVERT: D 288 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6995 (mtm180) REVERT: D 454 HIS cc_start: 0.7446 (t70) cc_final: 0.7008 (t-90) REVERT: D 574 MET cc_start: 0.8740 (mmm) cc_final: 0.8458 (mtt) REVERT: D 699 CYS cc_start: 0.7569 (t) cc_final: 0.7293 (t) REVERT: D 849 ARG cc_start: 0.5339 (mtt180) cc_final: 0.4691 (ptm160) REVERT: D 937 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 948 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8588 (pp) REVERT: D 1141 ASP cc_start: 0.7715 (t0) cc_final: 0.7451 (t0) outliers start: 87 outliers final: 43 residues processed: 342 average time/residue: 0.4491 time to fit residues: 240.6598 Evaluate side-chains 301 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 250 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1161 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 197 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 30528 Z= 0.216 Angle : 0.538 9.231 41372 Z= 0.277 Chirality : 0.038 0.177 4676 Planarity : 0.004 0.041 5208 Dihedral : 4.177 19.230 4092 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.88 % Allowed : 9.03 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3672 helix: 1.36 (0.11), residues: 2368 sheet: -0.63 (0.32), residues: 208 loop : -2.48 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 214 HIS 0.004 0.001 HIS C 166 PHE 0.017 0.002 PHE D 793 TYR 0.016 0.001 TYR C 228 ARG 0.007 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 265 time to evaluate : 3.536 Fit side-chains REVERT: B 241 TYR cc_start: 0.6720 (m-80) cc_final: 0.6514 (m-80) REVERT: B 278 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7053 (tt) REVERT: B 400 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 454 HIS cc_start: 0.7326 (t-90) cc_final: 0.7020 (t-90) REVERT: B 699 CYS cc_start: 0.7444 (t) cc_final: 0.7182 (t) REVERT: B 849 ARG cc_start: 0.5495 (mtt180) cc_final: 0.4827 (ptm160) REVERT: B 937 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 948 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 1141 ASP cc_start: 0.7948 (t0) cc_final: 0.7517 (t0) REVERT: A 159 LEU cc_start: 0.8292 (mt) cc_final: 0.8091 (mt) REVERT: A 224 PHE cc_start: 0.8065 (m-80) cc_final: 0.7604 (m-80) REVERT: A 400 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 454 HIS cc_start: 0.7262 (t-90) cc_final: 0.6981 (t-90) REVERT: A 849 ARG cc_start: 0.5385 (mtt180) cc_final: 0.4736 (ptm160) REVERT: A 937 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 948 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8602 (pp) REVERT: A 1141 ASP cc_start: 0.7926 (t0) cc_final: 0.7474 (t0) REVERT: C 159 LEU cc_start: 0.8222 (mt) cc_final: 0.8014 (mt) REVERT: C 224 PHE cc_start: 0.7992 (m-80) cc_final: 0.7532 (m-80) REVERT: C 252 LEU cc_start: 0.7626 (tp) cc_final: 0.7217 (mp) REVERT: C 285 MET cc_start: 0.5857 (mmp) cc_final: 0.5137 (mmt) REVERT: C 288 ARG cc_start: 0.7284 (mtp180) cc_final: 0.6813 (mtm180) REVERT: C 400 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8222 (mp) REVERT: C 454 HIS cc_start: 0.7343 (t-90) cc_final: 0.7046 (t-90) REVERT: C 699 CYS cc_start: 0.7492 (t) cc_final: 0.7191 (t) REVERT: C 849 ARG cc_start: 0.5487 (mtt180) cc_final: 0.4787 (ptm160) REVERT: C 851 ARG cc_start: 0.4674 (mtt180) cc_final: 0.4264 (mtp85) REVERT: C 937 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8541 (mp) REVERT: C 948 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 1141 ASP cc_start: 0.7918 (t0) cc_final: 0.7463 (t0) REVERT: D 159 LEU cc_start: 0.8169 (mt) cc_final: 0.7965 (mt) REVERT: D 252 LEU cc_start: 0.7630 (tp) cc_final: 0.7225 (mp) REVERT: D 285 MET cc_start: 0.5894 (mmp) cc_final: 0.5599 (mmt) REVERT: D 400 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 454 HIS cc_start: 0.7370 (t70) cc_final: 0.7027 (t-90) REVERT: D 699 CYS cc_start: 0.7479 (t) cc_final: 0.7182 (t) REVERT: D 849 ARG cc_start: 0.5291 (mtt180) cc_final: 0.4649 (ptm160) REVERT: D 937 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8560 (mp) REVERT: D 948 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8535 (pp) REVERT: D 1141 ASP cc_start: 0.7949 (t0) cc_final: 0.7546 (t0) outliers start: 92 outliers final: 56 residues processed: 339 average time/residue: 0.4541 time to fit residues: 240.3367 Evaluate side-chains 315 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 246 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1064 GLU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 322 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 454 HIS ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30528 Z= 0.275 Angle : 0.567 10.021 41372 Z= 0.290 Chirality : 0.039 0.183 4676 Planarity : 0.004 0.042 5208 Dihedral : 4.155 19.200 4092 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.12 % Allowed : 9.31 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3672 helix: 1.59 (0.11), residues: 2364 sheet: -0.72 (0.32), residues: 216 loop : -2.45 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 680 HIS 0.003 0.001 HIS C1127 PHE 0.018 0.002 PHE A 793 TYR 0.014 0.001 TYR D 339 ARG 0.004 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 267 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7079 (tt) REVERT: B 400 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 454 HIS cc_start: 0.7403 (t-90) cc_final: 0.6956 (t-90) REVERT: B 699 CYS cc_start: 0.7469 (t) cc_final: 0.7214 (t) REVERT: B 849 ARG cc_start: 0.5519 (mtt180) cc_final: 0.4838 (ptm160) REVERT: B 937 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8674 (mp) REVERT: B 948 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 1141 ASP cc_start: 0.8028 (t0) cc_final: 0.7580 (t0) REVERT: A 159 LEU cc_start: 0.8332 (mt) cc_final: 0.8105 (mt) REVERT: A 224 PHE cc_start: 0.8096 (m-80) cc_final: 0.7818 (m-80) REVERT: A 252 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7282 (tt) REVERT: A 400 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 454 HIS cc_start: 0.7333 (t-90) cc_final: 0.6920 (t-90) REVERT: A 849 ARG cc_start: 0.5402 (mtt180) cc_final: 0.4745 (ptm160) REVERT: A 937 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 948 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8641 (pp) REVERT: A 1141 ASP cc_start: 0.7997 (t0) cc_final: 0.7535 (t0) REVERT: C 224 PHE cc_start: 0.7987 (m-80) cc_final: 0.7786 (m-80) REVERT: C 252 LEU cc_start: 0.7691 (tp) cc_final: 0.7271 (mp) REVERT: C 285 MET cc_start: 0.5944 (mmp) cc_final: 0.5731 (mmt) REVERT: C 400 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8204 (mp) REVERT: C 454 HIS cc_start: 0.7366 (t-90) cc_final: 0.7070 (t-90) REVERT: C 699 CYS cc_start: 0.7504 (t) cc_final: 0.7207 (t) REVERT: C 849 ARG cc_start: 0.5382 (mtt180) cc_final: 0.4702 (ptm160) REVERT: C 851 ARG cc_start: 0.4636 (mtt180) cc_final: 0.4284 (mtp85) REVERT: C 937 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 948 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8319 (pp) REVERT: C 1141 ASP cc_start: 0.7984 (t0) cc_final: 0.7542 (t0) REVERT: D 159 LEU cc_start: 0.8188 (mt) cc_final: 0.7955 (mt) REVERT: D 224 PHE cc_start: 0.7992 (m-80) cc_final: 0.7744 (m-80) REVERT: D 252 LEU cc_start: 0.7644 (tp) cc_final: 0.7219 (mp) REVERT: D 400 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8311 (mp) REVERT: D 454 HIS cc_start: 0.7375 (t-90) cc_final: 0.7056 (t-90) REVERT: D 699 CYS cc_start: 0.7465 (t) cc_final: 0.7183 (t) REVERT: D 849 ARG cc_start: 0.5304 (mtt180) cc_final: 0.4653 (ptm160) REVERT: D 937 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 948 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8582 (pp) REVERT: D 1141 ASP cc_start: 0.7916 (t0) cc_final: 0.7459 (t0) outliers start: 100 outliers final: 76 residues processed: 346 average time/residue: 0.4238 time to fit residues: 233.7525 Evaluate side-chains 341 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 251 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1064 GLU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 359 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30528 Z= 0.163 Angle : 0.492 8.501 41372 Z= 0.254 Chirality : 0.037 0.177 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.914 19.067 4092 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.81 % Allowed : 10.00 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3672 helix: 1.97 (0.11), residues: 2368 sheet: -1.06 (0.32), residues: 236 loop : -2.28 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1123 HIS 0.004 0.001 HIS B 166 PHE 0.020 0.001 PHE D 113 TYR 0.012 0.001 TYR C 339 ARG 0.003 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 297 time to evaluate : 3.845 Fit side-chains REVERT: B 94 LEU cc_start: 0.8230 (mt) cc_final: 0.7890 (pt) REVERT: B 278 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7064 (tt) REVERT: B 400 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 454 HIS cc_start: 0.7337 (t-90) cc_final: 0.6861 (t-90) REVERT: B 699 CYS cc_start: 0.7316 (t) cc_final: 0.7024 (t) REVERT: B 849 ARG cc_start: 0.5231 (mtt180) cc_final: 0.4681 (ptm160) REVERT: B 948 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 1141 ASP cc_start: 0.7931 (t0) cc_final: 0.7514 (t0) REVERT: A 94 LEU cc_start: 0.8277 (mt) cc_final: 0.7986 (pt) REVERT: A 224 PHE cc_start: 0.8023 (m-80) cc_final: 0.7801 (m-80) REVERT: A 285 MET cc_start: 0.6048 (mmm) cc_final: 0.5751 (mmm) REVERT: A 400 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 454 HIS cc_start: 0.7273 (t-90) cc_final: 0.6845 (t-90) REVERT: A 849 ARG cc_start: 0.5196 (mtt180) cc_final: 0.4647 (ptm160) REVERT: A 948 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8502 (pp) REVERT: A 1141 ASP cc_start: 0.7932 (t0) cc_final: 0.7618 (t0) REVERT: C 94 LEU cc_start: 0.8191 (mt) cc_final: 0.7843 (pt) REVERT: C 224 PHE cc_start: 0.7968 (m-80) cc_final: 0.7742 (m-80) REVERT: C 252 LEU cc_start: 0.7720 (tp) cc_final: 0.7302 (mp) REVERT: C 285 MET cc_start: 0.5938 (mmp) cc_final: 0.5715 (mmt) REVERT: C 400 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8234 (mp) REVERT: C 454 HIS cc_start: 0.7385 (t-90) cc_final: 0.7100 (t-90) REVERT: C 699 CYS cc_start: 0.7354 (t) cc_final: 0.7024 (t) REVERT: C 849 ARG cc_start: 0.5340 (mtt180) cc_final: 0.4712 (ptm160) REVERT: C 851 ARG cc_start: 0.4731 (mtt180) cc_final: 0.4323 (mtp85) REVERT: C 948 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8091 (pp) REVERT: C 988 ASN cc_start: 0.7660 (t0) cc_final: 0.7316 (t0) REVERT: C 1141 ASP cc_start: 0.7930 (t0) cc_final: 0.7620 (t0) REVERT: D 224 PHE cc_start: 0.7956 (m-80) cc_final: 0.7723 (m-80) REVERT: D 252 LEU cc_start: 0.7734 (tp) cc_final: 0.7337 (mp) REVERT: D 400 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8175 (mp) REVERT: D 454 HIS cc_start: 0.7373 (t-90) cc_final: 0.7091 (t-90) REVERT: D 699 CYS cc_start: 0.7329 (t) cc_final: 0.7012 (t) REVERT: D 849 ARG cc_start: 0.5221 (mtt180) cc_final: 0.4614 (ptm160) REVERT: D 948 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8429 (pp) REVERT: D 1141 ASP cc_start: 0.7886 (t0) cc_final: 0.7547 (t0) outliers start: 90 outliers final: 61 residues processed: 365 average time/residue: 0.4417 time to fit residues: 252.7132 Evaluate side-chains 332 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 262 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1071 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1071 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 358 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30528 Z= 0.170 Angle : 0.495 8.764 41372 Z= 0.254 Chirality : 0.037 0.181 4676 Planarity : 0.004 0.038 5208 Dihedral : 3.825 18.699 4092 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.00 % Allowed : 9.69 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3672 helix: 2.10 (0.11), residues: 2368 sheet: -0.92 (0.31), residues: 236 loop : -2.27 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1123 HIS 0.003 0.001 HIS B 166 PHE 0.011 0.001 PHE B 793 TYR 0.012 0.001 TYR C 339 ARG 0.005 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 285 time to evaluate : 3.394 Fit side-chains REVERT: B 94 LEU cc_start: 0.8211 (mt) cc_final: 0.7907 (pt) REVERT: B 278 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7040 (tt) REVERT: B 400 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 454 HIS cc_start: 0.7330 (t-90) cc_final: 0.6850 (t-90) REVERT: B 699 CYS cc_start: 0.7274 (t) cc_final: 0.6989 (t) REVERT: B 849 ARG cc_start: 0.5234 (mtt180) cc_final: 0.4708 (ptm160) REVERT: B 948 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 1141 ASP cc_start: 0.7950 (t0) cc_final: 0.7556 (t0) REVERT: A 165 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5826 (mtp-110) REVERT: A 224 PHE cc_start: 0.7979 (m-80) cc_final: 0.7597 (m-10) REVERT: A 400 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 454 HIS cc_start: 0.7261 (t-90) cc_final: 0.6820 (t-90) REVERT: A 849 ARG cc_start: 0.5212 (mtt180) cc_final: 0.4678 (ptm160) REVERT: A 948 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 1141 ASP cc_start: 0.7946 (t0) cc_final: 0.7618 (t0) REVERT: C 94 LEU cc_start: 0.8175 (mt) cc_final: 0.7843 (pt) REVERT: C 224 PHE cc_start: 0.7968 (m-80) cc_final: 0.7730 (m-80) REVERT: C 252 LEU cc_start: 0.7679 (tp) cc_final: 0.7263 (mp) REVERT: C 400 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8234 (mp) REVERT: C 454 HIS cc_start: 0.7388 (t-90) cc_final: 0.7107 (t-90) REVERT: C 699 CYS cc_start: 0.7306 (t) cc_final: 0.6987 (t) REVERT: C 849 ARG cc_start: 0.5167 (mtt180) cc_final: 0.4610 (ptm160) REVERT: C 851 ARG cc_start: 0.4749 (mtt180) cc_final: 0.4380 (mtp-110) REVERT: C 948 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8138 (pp) REVERT: C 1141 ASP cc_start: 0.7960 (t0) cc_final: 0.7636 (t0) REVERT: D 252 LEU cc_start: 0.7736 (tp) cc_final: 0.7330 (mp) REVERT: D 400 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8258 (mp) REVERT: D 454 HIS cc_start: 0.7407 (t-90) cc_final: 0.7124 (t-90) REVERT: D 699 CYS cc_start: 0.7258 (t) cc_final: 0.6946 (t) REVERT: D 849 ARG cc_start: 0.5114 (mtt180) cc_final: 0.4585 (ptm160) REVERT: D 948 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8409 (pp) REVERT: D 1141 ASP cc_start: 0.7890 (t0) cc_final: 0.7526 (t0) outliers start: 96 outliers final: 67 residues processed: 359 average time/residue: 0.4627 time to fit residues: 261.5007 Evaluate side-chains 344 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 267 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1071 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1071 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN D1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 30528 Z= 0.225 Angle : 0.528 9.502 41372 Z= 0.270 Chirality : 0.038 0.176 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.880 18.875 4092 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.81 % Allowed : 10.09 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3672 helix: 2.07 (0.11), residues: 2372 sheet: -0.85 (0.32), residues: 236 loop : -2.28 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.003 0.001 HIS C1127 PHE 0.013 0.002 PHE A 793 TYR 0.012 0.001 TYR C 339 ARG 0.008 0.000 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 266 time to evaluate : 3.307 Fit side-chains REVERT: B 94 LEU cc_start: 0.8194 (mt) cc_final: 0.7899 (pt) REVERT: B 278 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7024 (tt) REVERT: B 400 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8252 (mp) REVERT: B 454 HIS cc_start: 0.7421 (t-90) cc_final: 0.6959 (t-90) REVERT: B 699 CYS cc_start: 0.7322 (t) cc_final: 0.7037 (t) REVERT: B 849 ARG cc_start: 0.5309 (mtt180) cc_final: 0.4728 (ptm160) REVERT: B 851 ARG cc_start: 0.4778 (mtt180) cc_final: 0.4426 (mtp-110) REVERT: B 937 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 948 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8528 (pp) REVERT: B 1141 ASP cc_start: 0.7961 (t0) cc_final: 0.7565 (t0) REVERT: A 159 LEU cc_start: 0.8343 (mt) cc_final: 0.8129 (mt) REVERT: A 165 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5906 (mtp-110) REVERT: A 224 PHE cc_start: 0.8023 (m-80) cc_final: 0.7725 (m-80) REVERT: A 400 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 454 HIS cc_start: 0.7336 (t-90) cc_final: 0.6900 (t-90) REVERT: A 849 ARG cc_start: 0.5314 (mtt180) cc_final: 0.4740 (ptm160) REVERT: A 851 ARG cc_start: 0.4607 (mtt180) cc_final: 0.4287 (mtp-110) REVERT: A 937 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8687 (mp) REVERT: A 948 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8560 (pp) REVERT: A 1141 ASP cc_start: 0.7985 (t0) cc_final: 0.7641 (t0) REVERT: C 94 LEU cc_start: 0.8147 (mt) cc_final: 0.7845 (pt) REVERT: C 224 PHE cc_start: 0.8004 (m-80) cc_final: 0.7794 (m-80) REVERT: C 252 LEU cc_start: 0.7734 (tp) cc_final: 0.7311 (mp) REVERT: C 400 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8248 (mp) REVERT: C 454 HIS cc_start: 0.7408 (t-90) cc_final: 0.7127 (t-90) REVERT: C 699 CYS cc_start: 0.7355 (t) cc_final: 0.7036 (t) REVERT: C 849 ARG cc_start: 0.5188 (mtt180) cc_final: 0.4664 (ptm160) REVERT: C 851 ARG cc_start: 0.4660 (mtt180) cc_final: 0.4323 (mtp-110) REVERT: C 948 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (pp) REVERT: C 988 ASN cc_start: 0.7745 (t0) cc_final: 0.7399 (t0) REVERT: C 1141 ASP cc_start: 0.8049 (t0) cc_final: 0.7671 (t0) REVERT: D 224 PHE cc_start: 0.7693 (m-80) cc_final: 0.7461 (m-80) REVERT: D 252 LEU cc_start: 0.7750 (tp) cc_final: 0.7348 (mp) REVERT: D 400 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 454 HIS cc_start: 0.7348 (t-90) cc_final: 0.6872 (t-90) REVERT: D 699 CYS cc_start: 0.7303 (t) cc_final: 0.6994 (t) REVERT: D 849 ARG cc_start: 0.5214 (mtt180) cc_final: 0.4644 (ptm160) REVERT: D 937 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8561 (mp) REVERT: D 948 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8497 (pp) REVERT: D 1141 ASP cc_start: 0.7951 (t0) cc_final: 0.7427 (t0) outliers start: 90 outliers final: 68 residues processed: 337 average time/residue: 0.4434 time to fit residues: 232.4880 Evaluate side-chains 341 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 260 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1064 GLU Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1071 LEU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1071 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 301 optimal weight: 0.0040 chunk 316 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C1013 ASN D1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30528 Z= 0.242 Angle : 0.546 9.667 41372 Z= 0.278 Chirality : 0.039 0.174 4676 Planarity : 0.004 0.040 5208 Dihedral : 3.922 18.990 4092 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.66 % Allowed : 10.31 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3672 helix: 2.06 (0.11), residues: 2372 sheet: -0.42 (0.33), residues: 216 loop : -2.34 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 680 HIS 0.003 0.001 HIS C 166 PHE 0.014 0.002 PHE A 415 TYR 0.012 0.001 TYR C 339 ARG 0.007 0.000 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 262 time to evaluate : 3.466 Fit side-chains REVERT: B 278 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7026 (tt) REVERT: B 400 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 454 HIS cc_start: 0.7374 (t-90) cc_final: 0.7158 (t70) REVERT: B 699 CYS cc_start: 0.7337 (t) cc_final: 0.7056 (t) REVERT: B 849 ARG cc_start: 0.5241 (mtt180) cc_final: 0.4741 (ptm160) REVERT: B 851 ARG cc_start: 0.4777 (mtt180) cc_final: 0.4427 (mtp-110) REVERT: B 937 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8693 (mp) REVERT: B 948 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 1141 ASP cc_start: 0.7974 (t0) cc_final: 0.7572 (t0) REVERT: A 165 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5918 (mtp-110) REVERT: A 224 PHE cc_start: 0.8036 (m-80) cc_final: 0.7752 (m-80) REVERT: A 252 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7313 (tt) REVERT: A 400 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 454 HIS cc_start: 0.7310 (t-90) cc_final: 0.6909 (t-90) REVERT: A 849 ARG cc_start: 0.5206 (mtt180) cc_final: 0.4708 (ptm160) REVERT: A 851 ARG cc_start: 0.4613 (mtt180) cc_final: 0.4292 (mtp-110) REVERT: A 937 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 948 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 1141 ASP cc_start: 0.8051 (t0) cc_final: 0.7661 (t0) REVERT: C 241 TYR cc_start: 0.6530 (m-80) cc_final: 0.6196 (m-80) REVERT: C 252 LEU cc_start: 0.7738 (tp) cc_final: 0.7319 (mp) REVERT: C 400 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 454 HIS cc_start: 0.7359 (t-90) cc_final: 0.7086 (t-90) REVERT: C 699 CYS cc_start: 0.7369 (t) cc_final: 0.7052 (t) REVERT: C 849 ARG cc_start: 0.5199 (mtt180) cc_final: 0.4669 (ptm160) REVERT: C 851 ARG cc_start: 0.4674 (mtt180) cc_final: 0.4330 (mtp-110) REVERT: C 948 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8214 (pp) REVERT: C 1141 ASP cc_start: 0.8049 (t0) cc_final: 0.7659 (t0) REVERT: D 252 LEU cc_start: 0.7756 (tp) cc_final: 0.7339 (mp) REVERT: D 400 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8181 (mp) REVERT: D 454 HIS cc_start: 0.7366 (t-90) cc_final: 0.6927 (t-90) REVERT: D 699 CYS cc_start: 0.7323 (t) cc_final: 0.7020 (t) REVERT: D 849 ARG cc_start: 0.5222 (mtt180) cc_final: 0.4650 (ptm160) REVERT: D 851 ARG cc_start: 0.4542 (mtt180) cc_final: 0.4199 (mtp-110) REVERT: D 937 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 948 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8507 (pp) REVERT: D 1141 ASP cc_start: 0.7945 (t0) cc_final: 0.7415 (t0) outliers start: 85 outliers final: 63 residues processed: 326 average time/residue: 0.4519 time to fit residues: 228.6925 Evaluate side-chains 337 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 260 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1064 GLU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 370 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 295 optimal weight: 0.0060 chunk 30 optimal weight: 0.2980 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30528 Z= 0.124 Angle : 0.471 7.890 41372 Z= 0.243 Chirality : 0.036 0.166 4676 Planarity : 0.003 0.037 5208 Dihedral : 3.668 18.371 4092 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.78 % Allowed : 11.38 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.14), residues: 3672 helix: 2.37 (0.11), residues: 2380 sheet: -0.32 (0.33), residues: 216 loop : -2.24 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1014 HIS 0.004 0.001 HIS B 166 PHE 0.011 0.001 PHE A 627 TYR 0.010 0.001 TYR B 964 ARG 0.007 0.000 ARG D 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 317 time to evaluate : 3.346 Fit side-chains revert: symmetry clash REVERT: B 278 LEU cc_start: 0.7215 (tp) cc_final: 0.6987 (tt) REVERT: B 400 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8245 (mp) REVERT: B 454 HIS cc_start: 0.7330 (t-90) cc_final: 0.7029 (t-90) REVERT: B 480 GLN cc_start: 0.7989 (mt0) cc_final: 0.7616 (mt0) REVERT: B 699 CYS cc_start: 0.7016 (t) cc_final: 0.6781 (t) REVERT: B 849 ARG cc_start: 0.5133 (mtt180) cc_final: 0.4672 (ptm160) REVERT: B 851 ARG cc_start: 0.4795 (mtt180) cc_final: 0.4423 (mtp-110) REVERT: B 988 ASN cc_start: 0.7597 (t0) cc_final: 0.7236 (t0) REVERT: B 1141 ASP cc_start: 0.7942 (t0) cc_final: 0.7588 (t0) REVERT: A 165 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5851 (mtp-110) REVERT: A 224 PHE cc_start: 0.7876 (m-80) cc_final: 0.7426 (m-10) REVERT: A 400 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 454 HIS cc_start: 0.7260 (t-90) cc_final: 0.6813 (t-90) REVERT: A 480 GLN cc_start: 0.8008 (mt0) cc_final: 0.7671 (mt0) REVERT: A 849 ARG cc_start: 0.5091 (mtt180) cc_final: 0.4597 (ptm160) REVERT: A 851 ARG cc_start: 0.4711 (mtt180) cc_final: 0.4370 (mtp-110) REVERT: A 1141 ASP cc_start: 0.7978 (t0) cc_final: 0.7636 (t0) REVERT: C 224 PHE cc_start: 0.7685 (m-80) cc_final: 0.7290 (m-80) REVERT: C 241 TYR cc_start: 0.6303 (m-80) cc_final: 0.5977 (m-80) REVERT: C 252 LEU cc_start: 0.7660 (tp) cc_final: 0.7267 (mp) REVERT: C 400 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8222 (mp) REVERT: C 454 HIS cc_start: 0.7373 (t-90) cc_final: 0.7104 (t-90) REVERT: C 480 GLN cc_start: 0.7978 (mt0) cc_final: 0.7596 (mt0) REVERT: C 699 CYS cc_start: 0.7037 (t) cc_final: 0.6770 (t) REVERT: C 849 ARG cc_start: 0.5019 (mtt180) cc_final: 0.4590 (ptm160) REVERT: C 851 ARG cc_start: 0.4744 (mtt180) cc_final: 0.4402 (mtp-110) REVERT: C 948 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7967 (pp) REVERT: C 988 ASN cc_start: 0.7592 (t0) cc_final: 0.7238 (t0) REVERT: C 1141 ASP cc_start: 0.7996 (t0) cc_final: 0.7479 (t0) REVERT: D 252 LEU cc_start: 0.7681 (tp) cc_final: 0.7285 (mp) REVERT: D 400 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8253 (mp) REVERT: D 454 HIS cc_start: 0.7331 (t-90) cc_final: 0.6847 (t-90) REVERT: D 480 GLN cc_start: 0.7980 (mt0) cc_final: 0.7599 (mt0) REVERT: D 699 CYS cc_start: 0.7001 (t) cc_final: 0.6604 (t) REVERT: D 849 ARG cc_start: 0.5014 (mtt180) cc_final: 0.4519 (ptm160) REVERT: D 851 ARG cc_start: 0.4639 (mtt180) cc_final: 0.4272 (mtp-110) REVERT: D 988 ASN cc_start: 0.7577 (t0) cc_final: 0.7217 (t0) REVERT: D 1141 ASP cc_start: 0.7939 (t0) cc_final: 0.7398 (t0) outliers start: 57 outliers final: 41 residues processed: 363 average time/residue: 0.4437 time to fit residues: 250.9080 Evaluate side-chains 326 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 279 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 295 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135223 restraints weight = 40586.569| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.48 r_work: 0.3250 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30528 Z= 0.189 Angle : 0.517 8.648 41372 Z= 0.264 Chirality : 0.038 0.179 4676 Planarity : 0.004 0.039 5208 Dihedral : 3.713 18.513 4092 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.03 % Allowed : 11.16 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.14), residues: 3672 helix: 2.32 (0.11), residues: 2380 sheet: -0.25 (0.33), residues: 216 loop : -2.24 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.004 0.001 HIS C 166 PHE 0.012 0.001 PHE A 415 TYR 0.013 0.001 TYR D 855 ARG 0.009 0.000 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6377.66 seconds wall clock time: 115 minutes 50.46 seconds (6950.46 seconds total)