Starting phenix.real_space_refine on Thu Mar 5 00:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl7_25193/03_2026/7sl7_25193.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 9350 2.51 5 N 2524 2.21 5 O 2734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14732 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "G" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "I" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 2.98, per 1000 atoms: 0.20 Number of scatterers: 14732 At special positions: 0 Unit cell: (120.35, 130.31, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 2734 8.00 N 2524 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS H 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 527.6 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 33 sheets defined 19.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.788A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.755A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.740A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.731A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.679A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.577A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.758A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.543A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.555A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 646 removed outlier: 4.002A pdb=" N LEU A 646 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 716 removed outlier: 3.659A pdb=" N ILE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.839A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.741A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.746A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.730A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.584A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.727A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.569A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.558A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.999A pdb=" N LEU B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 716 removed outlier: 3.630A pdb=" N ILE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'H' and resid 8 through 19 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'J' and resid 8 through 19 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.688A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.533A pdb=" N GLU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 18 " --> pdb=" O TYR E 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 13 through 18' Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 removed outlier: 3.758A pdb=" N GLU F 17 " --> pdb=" O TYR F 14 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.508A pdb=" N GLN A 34 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.549A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AB1, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.687A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB3, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.628A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 601 through 606 removed outlier: 5.447A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 765 removed outlier: 3.759A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 removed outlier: 4.107A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 907 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 11 through 14 removed outlier: 3.509A pdb=" N GLN B 34 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.566A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.570A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.679A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.643A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.392A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 613 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 765 removed outlier: 3.808A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.511A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 907 " --> pdb=" O GLY B 882 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 966 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: 2.39 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4822 1.34 - 1.46: 3506 1.46 - 1.58: 6609 1.58 - 1.70: 1 1.70 - 1.82: 148 Bond restraints: 15086 Sorted by residual: bond pdb=" CB PRO B 720 " pdb=" CG PRO B 720 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.96e+00 bond pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 1.526 1.511 0.014 1.36e-02 5.41e+03 1.13e+00 bond pdb=" CB GLU B 6 " pdb=" CG GLU B 6 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" C GLN E 5 " pdb=" N CYS E 6 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.42e-02 4.96e+03 8.68e-01 ... (remaining 15081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 20159 2.10 - 4.20: 260 4.20 - 6.30: 16 6.30 - 8.40: 3 8.40 - 10.49: 2 Bond angle restraints: 20440 Sorted by residual: angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N GLY I 8 " pdb=" CA GLY I 8 " pdb=" C GLY I 8 " ideal model delta sigma weight residual 111.35 115.50 -4.15 1.20e+00 6.94e-01 1.20e+01 ... (remaining 20435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 8212 16.10 - 32.21: 692 32.21 - 48.31: 174 48.31 - 64.41: 42 64.41 - 80.51: 26 Dihedral angle restraints: 9146 sinusoidal: 3816 harmonic: 5330 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.92 -77.92 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 6 " pdb=" SG CYS E 6 " pdb=" SG CYS E 11 " pdb=" CB CYS E 11 " ideal model delta sinusoidal sigma weight residual 93.00 39.14 53.86 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 9143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1464 0.036 - 0.072: 518 0.072 - 0.108: 153 0.108 - 0.144: 75 0.144 - 0.180: 6 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 2213 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C THR A 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 836 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 837 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 837 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 837 " 0.024 5.00e-02 4.00e+02 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 358 2.70 - 3.25: 14045 3.25 - 3.80: 22611 3.80 - 4.35: 30781 4.35 - 4.90: 50028 Nonbonded interactions: 117823 Sorted by model distance: nonbonded pdb=" O ASP A 535 " pdb=" OH TYR E 14 " model vdw 2.149 3.040 nonbonded pdb=" O ASP B 535 " pdb=" OH TYR F 14 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG A 889 " pdb=" OG1 THR A 891 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG B 889 " pdb=" OG1 THR B 891 " model vdw 2.243 3.120 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.266 3.040 ... (remaining 117818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'D' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'E' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'F' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ } ncs_group { reference = (chain 'G' and resid 2 through 26) selection = (chain 'H' and resid 2 through 26) selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.002 0.099 15132 Z= 0.108 Angle : 0.566 10.495 20532 Z= 0.304 Chirality : 0.044 0.180 2216 Planarity : 0.003 0.044 2642 Dihedral : 13.076 80.513 5568 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 0.24 % Allowed : 0.54 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1782 helix: -0.31 (0.34), residues: 242 sheet: 0.45 (0.31), residues: 368 loop : -0.99 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 759 TYR 0.012 0.001 TYR A 507 PHE 0.021 0.001 PHE A 574 TRP 0.006 0.001 TRP B 414 HIS 0.003 0.000 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00237 (15086) covalent geometry : angle 0.56484 (20440) SS BOND : bond 0.00195 ( 46) SS BOND : angle 0.83692 ( 92) hydrogen bonds : bond 0.24575 ( 375) hydrogen bonds : angle 8.40090 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 867 HIS cc_start: 0.7477 (m90) cc_final: 0.7177 (m90) outliers start: 4 outliers final: 1 residues processed: 146 average time/residue: 0.0932 time to fit residues: 22.0691 Evaluate side-chains 102 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS J 3 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.119404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082369 restraints weight = 35694.266| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.23 r_work: 0.3295 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15132 Z= 0.142 Angle : 0.576 6.969 20532 Z= 0.301 Chirality : 0.045 0.171 2216 Planarity : 0.003 0.044 2642 Dihedral : 4.627 36.961 1994 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 1.02 % Allowed : 6.08 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1782 helix: 0.23 (0.35), residues: 236 sheet: 0.66 (0.31), residues: 338 loop : -0.95 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.019 0.001 TYR A 507 PHE 0.013 0.001 PHE B 567 TRP 0.008 0.001 TRP A 899 HIS 0.014 0.001 HIS J 5 Details of bonding type rmsd covalent geometry : bond 0.00336 (15086) covalent geometry : angle 0.57209 (20440) SS BOND : bond 0.00286 ( 46) SS BOND : angle 1.11031 ( 92) hydrogen bonds : bond 0.04380 ( 375) hydrogen bonds : angle 6.29133 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7617 (tpt) cc_final: 0.7322 (tpt) REVERT: A 763 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7749 (ttmt) REVERT: A 867 HIS cc_start: 0.7389 (m90) cc_final: 0.7077 (m90) REVERT: B 300 MET cc_start: 0.7671 (tpt) cc_final: 0.7360 (tpt) REVERT: B 763 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7866 (ttmt) REVERT: I 11 LEU cc_start: 0.8488 (mt) cc_final: 0.8283 (mp) REVERT: J 11 LEU cc_start: 0.8475 (mt) cc_final: 0.8259 (mp) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.0953 time to fit residues: 17.8654 Evaluate side-chains 111 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 145 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: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080581 restraints weight = 36172.732| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.29 r_work: 0.3253 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15132 Z= 0.151 Angle : 0.548 6.076 20532 Z= 0.287 Chirality : 0.044 0.172 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.627 29.324 1992 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 0.96 % Allowed : 8.30 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1782 helix: 0.09 (0.34), residues: 246 sheet: 0.41 (0.29), residues: 362 loop : -0.94 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.020 0.001 TYR B 507 PHE 0.020 0.001 PHE A 574 TRP 0.008 0.001 TRP A 899 HIS 0.005 0.001 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00361 (15086) covalent geometry : angle 0.54477 (20440) SS BOND : bond 0.00299 ( 46) SS BOND : angle 1.05069 ( 92) hydrogen bonds : bond 0.03898 ( 375) hydrogen bonds : angle 5.84682 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.575 Fit side-chains REVERT: A 867 HIS cc_start: 0.7432 (m90) cc_final: 0.7097 (m90) REVERT: C 17 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8230 (tm-30) outliers start: 16 outliers final: 8 residues processed: 113 average time/residue: 0.0952 time to fit residues: 17.3807 Evaluate side-chains 104 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN I 3 ASN J 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.114664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077528 restraints weight = 35755.772| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.24 r_work: 0.3187 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15132 Z= 0.254 Angle : 0.644 8.085 20532 Z= 0.332 Chirality : 0.047 0.227 2216 Planarity : 0.004 0.044 2642 Dihedral : 5.065 25.992 1992 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.74 % Favored : 92.14 % Rotamer: Outliers : 1.32 % Allowed : 11.61 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1782 helix: 0.08 (0.34), residues: 242 sheet: 0.26 (0.29), residues: 352 loop : -1.04 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 759 TYR 0.023 0.002 TYR B 430 PHE 0.017 0.002 PHE A 567 TRP 0.016 0.001 TRP B 899 HIS 0.005 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00603 (15086) covalent geometry : angle 0.63740 (20440) SS BOND : bond 0.00459 ( 46) SS BOND : angle 1.52508 ( 92) hydrogen bonds : bond 0.04021 ( 375) hydrogen bonds : angle 5.93364 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9322 (mp) REVERT: A 300 MET cc_start: 0.8369 (mpp) cc_final: 0.7894 (tpt) REVERT: A 792 SER cc_start: 0.3432 (OUTLIER) cc_final: 0.3114 (t) REVERT: A 867 HIS cc_start: 0.7561 (m90) cc_final: 0.7209 (m90) REVERT: B 42 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7922 (mmm160) REVERT: B 300 MET cc_start: 0.8393 (mpp) cc_final: 0.7975 (tpt) REVERT: B 792 SER cc_start: 0.3576 (OUTLIER) cc_final: 0.3254 (t) REVERT: C 17 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8164 (tm-30) outliers start: 22 outliers final: 10 residues processed: 117 average time/residue: 0.1145 time to fit residues: 20.2549 Evaluate side-chains 102 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.117199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080429 restraints weight = 35694.138| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.22 r_work: 0.3245 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15132 Z= 0.115 Angle : 0.563 7.389 20532 Z= 0.295 Chirality : 0.044 0.186 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.805 28.418 1992 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 1.32 % Allowed : 12.76 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1782 helix: 0.10 (0.33), residues: 248 sheet: 0.24 (0.29), residues: 362 loop : -0.96 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 889 TYR 0.017 0.001 TYR A 581 PHE 0.016 0.001 PHE A 574 TRP 0.031 0.001 TRP A 899 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00272 (15086) covalent geometry : angle 0.55651 (20440) SS BOND : bond 0.00310 ( 46) SS BOND : angle 1.43349 ( 92) hydrogen bonds : bond 0.03538 ( 375) hydrogen bonds : angle 5.65356 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.562 Fit side-chains REVERT: A 300 MET cc_start: 0.8272 (mpp) cc_final: 0.7839 (tpt) REVERT: A 581 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 792 SER cc_start: 0.3578 (OUTLIER) cc_final: 0.3257 (t) REVERT: A 867 HIS cc_start: 0.7577 (m90) cc_final: 0.7227 (m90) REVERT: B 42 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8008 (mmm160) REVERT: B 581 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6554 (t80) REVERT: B 792 SER cc_start: 0.3668 (OUTLIER) cc_final: 0.3345 (t) REVERT: C 17 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8195 (tm-30) outliers start: 22 outliers final: 7 residues processed: 110 average time/residue: 0.0888 time to fit residues: 16.0446 Evaluate side-chains 99 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 HIS I 3 ASN J 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.116950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080068 restraints weight = 35706.050| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.29 r_work: 0.3244 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15132 Z= 0.126 Angle : 0.551 8.019 20532 Z= 0.287 Chirality : 0.044 0.180 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.677 27.409 1992 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 1.32 % Allowed : 13.30 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1782 helix: -0.27 (0.32), residues: 272 sheet: 0.27 (0.28), residues: 362 loop : -1.01 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.018 0.001 TYR A 581 PHE 0.017 0.001 PHE B 574 TRP 0.018 0.001 TRP A 899 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00303 (15086) covalent geometry : angle 0.54667 (20440) SS BOND : bond 0.00293 ( 46) SS BOND : angle 1.15055 ( 92) hydrogen bonds : bond 0.03407 ( 375) hydrogen bonds : angle 5.51507 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8005 (mmm160) REVERT: A 300 MET cc_start: 0.8375 (mpp) cc_final: 0.7902 (tpt) REVERT: A 581 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.6362 (t80) REVERT: A 792 SER cc_start: 0.3693 (OUTLIER) cc_final: 0.3312 (t) REVERT: A 867 HIS cc_start: 0.7529 (m90) cc_final: 0.7238 (m-70) REVERT: B 42 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8037 (mmm160) REVERT: B 300 MET cc_start: 0.8237 (mpp) cc_final: 0.7929 (tpt) REVERT: B 581 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6596 (t80) REVERT: B 792 SER cc_start: 0.3756 (OUTLIER) cc_final: 0.3385 (t) REVERT: C 17 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8202 (tm-30) outliers start: 22 outliers final: 10 residues processed: 112 average time/residue: 0.0940 time to fit residues: 17.3075 Evaluate side-chains 105 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.116803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.080007 restraints weight = 35512.138| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.27 r_work: 0.3238 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15132 Z= 0.130 Angle : 0.549 6.691 20532 Z= 0.286 Chirality : 0.044 0.175 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.746 28.299 1992 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.20 % Allowed : 13.78 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1782 helix: -0.25 (0.32), residues: 272 sheet: 0.42 (0.29), residues: 342 loop : -1.04 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.018 0.001 TYR A 581 PHE 0.014 0.001 PHE A 574 TRP 0.016 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00312 (15086) covalent geometry : angle 0.54284 (20440) SS BOND : bond 0.00265 ( 46) SS BOND : angle 1.36200 ( 92) hydrogen bonds : bond 0.03323 ( 375) hydrogen bonds : angle 5.43842 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8059 (mmm160) REVERT: A 581 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6318 (t80) REVERT: A 792 SER cc_start: 0.3711 (OUTLIER) cc_final: 0.3329 (t) REVERT: A 867 HIS cc_start: 0.7550 (m90) cc_final: 0.7260 (m-70) REVERT: B 42 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8046 (mmm160) REVERT: B 581 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 792 SER cc_start: 0.3797 (OUTLIER) cc_final: 0.3428 (t) REVERT: C 17 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8229 (tm-30) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.0927 time to fit residues: 16.6776 Evaluate side-chains 106 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 100 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.115737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078866 restraints weight = 35661.375| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.27 r_work: 0.3217 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15132 Z= 0.164 Angle : 0.566 6.720 20532 Z= 0.295 Chirality : 0.044 0.168 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.793 26.745 1992 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.08 % Allowed : 14.32 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1782 helix: -0.19 (0.32), residues: 272 sheet: 0.39 (0.29), residues: 342 loop : -1.05 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.021 0.001 TYR B 581 PHE 0.014 0.001 PHE A 567 TRP 0.016 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00392 (15086) covalent geometry : angle 0.56074 (20440) SS BOND : bond 0.00339 ( 46) SS BOND : angle 1.23917 ( 92) hydrogen bonds : bond 0.03431 ( 375) hydrogen bonds : angle 5.45402 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8048 (mmm160) REVERT: A 300 MET cc_start: 0.8280 (mpp) cc_final: 0.7986 (tpt) REVERT: A 581 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6326 (t80) REVERT: A 792 SER cc_start: 0.3780 (OUTLIER) cc_final: 0.3530 (m) REVERT: A 867 HIS cc_start: 0.7623 (m90) cc_final: 0.7310 (m-70) REVERT: B 42 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8045 (mmm160) REVERT: B 300 MET cc_start: 0.8230 (mpp) cc_final: 0.8021 (tpt) REVERT: B 581 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.6330 (t80) REVERT: C 17 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8244 (tm-30) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.0971 time to fit residues: 16.2665 Evaluate side-chains 104 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 27 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.116593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080291 restraints weight = 35539.678| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.24 r_work: 0.3247 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15132 Z= 0.107 Angle : 0.534 6.661 20532 Z= 0.279 Chirality : 0.043 0.157 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.636 26.567 1992 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.08 % Allowed : 14.26 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1782 helix: -0.01 (0.33), residues: 260 sheet: 0.46 (0.29), residues: 342 loop : -0.94 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.018 0.001 TYR A 581 PHE 0.014 0.001 PHE A 707 TRP 0.012 0.001 TRP A 899 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00255 (15086) covalent geometry : angle 0.53087 (20440) SS BOND : bond 0.00253 ( 46) SS BOND : angle 1.05221 ( 92) hydrogen bonds : bond 0.03174 ( 375) hydrogen bonds : angle 5.34694 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8059 (mmm160) REVERT: A 300 MET cc_start: 0.8212 (mpp) cc_final: 0.7867 (tpt) REVERT: A 581 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6245 (t80) REVERT: A 792 SER cc_start: 0.3875 (OUTLIER) cc_final: 0.3636 (m) REVERT: A 867 HIS cc_start: 0.7552 (m90) cc_final: 0.7252 (m-70) REVERT: B 42 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8063 (mmm160) REVERT: B 581 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6307 (t80) REVERT: C 17 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8248 (tm-30) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 0.0954 time to fit residues: 16.7399 Evaluate side-chains 105 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 113 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.117035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080513 restraints weight = 35537.764| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.26 r_work: 0.3255 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15132 Z= 0.110 Angle : 0.534 7.146 20532 Z= 0.279 Chirality : 0.043 0.157 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.553 25.873 1992 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.84 % Allowed : 14.56 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1782 helix: 0.04 (0.33), residues: 260 sheet: 0.49 (0.29), residues: 342 loop : -0.91 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 13 TYR 0.018 0.001 TYR A 581 PHE 0.014 0.001 PHE A 707 TRP 0.012 0.001 TRP A 899 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00262 (15086) covalent geometry : angle 0.53141 (20440) SS BOND : bond 0.00248 ( 46) SS BOND : angle 1.00006 ( 92) hydrogen bonds : bond 0.03245 ( 375) hydrogen bonds : angle 5.29940 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8066 (mmm160) REVERT: A 581 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6214 (t80) REVERT: A 867 HIS cc_start: 0.7603 (m90) cc_final: 0.7270 (m90) REVERT: B 42 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8069 (mmm160) REVERT: B 581 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6280 (t80) REVERT: C 17 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8260 (tm-30) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.0883 time to fit residues: 15.1759 Evaluate side-chains 106 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 132 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.115838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079107 restraints weight = 35576.466| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.25 r_work: 0.3219 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15132 Z= 0.159 Angle : 0.573 9.443 20532 Z= 0.297 Chirality : 0.044 0.157 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.744 26.223 1992 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.02 % Allowed : 14.44 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1782 helix: -0.17 (0.33), residues: 272 sheet: 0.48 (0.29), residues: 342 loop : -0.96 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 13 TYR 0.021 0.001 TYR A 581 PHE 0.014 0.001 PHE A 574 TRP 0.015 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00380 (15086) covalent geometry : angle 0.56682 (20440) SS BOND : bond 0.00309 ( 46) SS BOND : angle 1.36142 ( 92) hydrogen bonds : bond 0.03408 ( 375) hydrogen bonds : angle 5.36919 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.67 seconds wall clock time: 74 minutes 13.40 seconds (4453.40 seconds total)