Starting phenix.real_space_refine on Thu Feb 5 08:01:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.map" model { file = "/net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cin_45622/02_2026/9cin_45622.cif" } resolution = 3.03 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9981 2.51 5 N 2598 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15798 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3394 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 16, 'TRANS': 423} Chain breaks: 1 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "B" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3394 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 16, 'TRANS': 423} Chain breaks: 1 Chain: "C" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3394 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 16, 'TRANS': 423} Chain breaks: 1 Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15798 At special positions: 0 Unit cell: (123.75, 127.875, 129.525, 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 78 16.00 O 3141 8.00 N 2598 7.00 C 9981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.04 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 414 " " NAG A 602 " - " ASN A 99 " " NAG B 601 " - " ASN B 414 " " NAG B 602 " - " ASN B 99 " " NAG C 601 " - " ASN C 414 " " NAG C 602 " - " ASN C 99 " " NAG D 1 " - " ASN A 464 " " NAG E 1 " - " ASN A 67 " " NAG F 1 " - " ASN B 464 " " NAG G 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 464 " " NAG O 1 " - " ASN C 67 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 611.4 milliseconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 29 sheets defined 24.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 33 through 36 Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.599A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.555A pdb=" N LYS A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 100' Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.891A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.578A pdb=" N ASN A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 211 removed outlier: 3.549A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.816A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.578A pdb=" N CYS A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.638A pdb=" N LYS A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.925A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.668A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.645A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.652A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.611A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.656A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.579A pdb=" N ASP M 90 " --> pdb=" O ARG M 87 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 87 through 91' Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.588A pdb=" N LEU B 33 " --> pdb=" O HIS B 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Proline residue: B 89 - end of helix removed outlier: 4.765A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.648A pdb=" N GLY B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 121' Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.609A pdb=" N GLU B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.827A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 153' Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.803A pdb=" N ILE B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 211 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.183A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 358 removed outlier: 3.644A pdb=" N CYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.639A pdb=" N LYS B 362 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.882A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.583A pdb=" N LEU C 33 " --> pdb=" O HIS C 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Proline residue: C 89 - end of helix removed outlier: 4.747A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.562A pdb=" N GLY C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 121' Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.508A pdb=" N GLU C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.839A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 153' Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.816A pdb=" N ILE C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 211 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.138A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 358 removed outlier: 3.546A pdb=" N CYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.614A pdb=" N LYS C 362 " --> pdb=" O SER C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.815A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 40 current: chain 'A' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 173 current: chain 'A' and resid 263 through 270 removed outlier: 3.726A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 326 current: chain 'A' and resid 337 through 340 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.532A pdb=" N GLN C 393 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.725A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.689A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 426 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.906A pdb=" N ILE H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 97 through 99 removed outlier: 6.447A pdb=" N ARG H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.953A pdb=" N ILE J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 98 through 99 removed outlier: 4.092A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.880A pdb=" N ILE M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 98 through 99 removed outlier: 6.591A pdb=" N ARG M 98 " --> pdb=" O ASP M 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.641A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.728A pdb=" N THR L 103 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 38 through 40 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 40 current: chain 'B' and resid 168 through 173 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 173 current: chain 'B' and resid 263 through 270 removed outlier: 3.794A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 322 through 326 current: chain 'B' and resid 337 through 340 Processing sheet with id=AC2, first strand: chain 'B' and resid 301 through 302 removed outlier: 6.769A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'B' and resid 393 through 394 removed outlier: 3.553A pdb=" N GLN B 393 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 425 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 38 through 40 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 40 current: chain 'C' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 263 through 270 removed outlier: 3.788A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 326 current: chain 'C' and resid 337 through 340 Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.766A pdb=" N ARG C 365 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.633A pdb=" N ILE K 75 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.755A pdb=" N THR K 103 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.634A pdb=" N ILE N 75 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.615A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1338 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: 2.37 Time building geometry restraints manager: 1.59 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: 5013 1.34 - 1.47: 3795 1.47 - 1.59: 7158 1.59 - 1.72: 0 1.72 - 1.84: 111 Bond restraints: 16077 Sorted by residual: bond pdb=" C THR A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.56e+00 bond pdb=" C ILE A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.34e-02 5.57e+03 3.39e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.99e+00 bond pdb=" C SER N 7 " pdb=" N PRO N 8 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.97e+00 bond pdb=" C SER K 7 " pdb=" N PRO K 8 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 ... (remaining 16072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21124 1.85 - 3.69: 615 3.69 - 5.54: 68 5.54 - 7.39: 25 7.39 - 9.23: 8 Bond angle restraints: 21840 Sorted by residual: angle pdb=" C ASN B 464 " pdb=" N GLN B 465 " pdb=" CA GLN B 465 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C LEU A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 120.24 123.25 -3.01 6.30e-01 2.52e+00 2.28e+01 angle pdb=" C ASN C 464 " pdb=" N GLN C 465 " pdb=" CA GLN C 465 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" N ILE A 96 " pdb=" CA ILE A 96 " pdb=" C ILE A 96 " ideal model delta sigma weight residual 110.72 106.55 4.17 1.01e+00 9.80e-01 1.71e+01 angle pdb=" N VAL A 75 " pdb=" CA VAL A 75 " pdb=" C VAL A 75 " ideal model delta sigma weight residual 112.12 108.73 3.39 8.40e-01 1.42e+00 1.63e+01 ... (remaining 21835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9185 17.99 - 35.98: 694 35.98 - 53.96: 140 53.96 - 71.95: 19 71.95 - 89.94: 18 Dihedral angle restraints: 10056 sinusoidal: 4221 harmonic: 5835 Sorted by residual: dihedral pdb=" CA GLN B 465 " pdb=" C GLN B 465 " pdb=" N SER B 466 " pdb=" CA SER B 466 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLN C 465 " pdb=" C GLN C 465 " pdb=" N SER C 466 " pdb=" CA SER C 466 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual 93.00 138.56 -45.56 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 10053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2042 0.058 - 0.117: 485 0.117 - 0.175: 92 0.175 - 0.234: 5 0.234 - 0.292: 1 Chirality restraints: 2625 Sorted by residual: chirality pdb=" CB ILE A 179 " pdb=" CA ILE A 179 " pdb=" CG1 ILE A 179 " pdb=" CG2 ILE A 179 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 36 " pdb=" CA ILE A 36 " pdb=" CG1 ILE A 36 " pdb=" CG2 ILE A 36 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLN B 465 " pdb=" N GLN B 465 " pdb=" C GLN B 465 " pdb=" CB GLN B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 2622 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 67 " -0.021 2.00e-02 2.50e+03 1.96e-02 4.80e+00 pdb=" CG ASN B 67 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 67 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 67 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 347 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 346 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO B 347 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " 0.026 5.00e-02 4.00e+02 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 7111 2.99 - 3.47: 14338 3.47 - 3.94: 24928 3.94 - 4.42: 27775 4.42 - 4.90: 47728 Nonbonded interactions: 121880 Sorted by model distance: nonbonded pdb=" O5 NAG E 1 " pdb=" O6 NAG E 1 " model vdw 2.509 2.432 nonbonded pdb=" N ILE A 190 " pdb=" O ILE A 190 " model vdw 2.587 2.496 nonbonded pdb=" N THR A 227 " pdb=" OG1 THR A 227 " model vdw 2.599 2.496 nonbonded pdb=" N THR C 227 " pdb=" OG1 THR C 227 " model vdw 2.602 2.496 nonbonded pdb=" N THR B 227 " pdb=" OG1 THR B 227 " model vdw 2.603 2.496 ... (remaining 121875 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.230 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16122 Z= 0.184 Angle : 0.764 11.220 21954 Z= 0.410 Chirality : 0.052 0.292 2625 Planarity : 0.005 0.047 2745 Dihedral : 13.131 89.941 6255 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.23 % Allowed : 2.58 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -2.26 (0.18), residues: 1983 helix: -3.56 (0.15), residues: 378 sheet: 0.19 (0.23), residues: 570 loop : -1.66 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 365 TYR 0.018 0.001 TYR A 46 PHE 0.011 0.002 PHE A 301 TRP 0.012 0.002 TRP B 308 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00388 (16077) covalent geometry : angle 0.74673 (21840) SS BOND : bond 0.00534 ( 21) SS BOND : angle 1.31005 ( 42) hydrogen bonds : bond 0.22579 ( 504) hydrogen bonds : angle 8.96196 ( 1338) link_ALPHA1-3 : bond 0.01360 ( 3) link_ALPHA1-3 : angle 1.39651 ( 9) link_BETA1-4 : bond 0.00801 ( 9) link_BETA1-4 : angle 2.72147 ( 27) link_NAG-ASN : bond 0.00700 ( 12) link_NAG-ASN : angle 3.14506 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.506 Fit side-chains REVERT: A 74 SER cc_start: 0.8313 (m) cc_final: 0.7747 (t) REVERT: A 78 ASN cc_start: 0.8572 (m110) cc_final: 0.8371 (m110) REVERT: A 96 ILE cc_start: 0.8562 (mp) cc_final: 0.7987 (mm) REVERT: A 103 ASP cc_start: 0.8118 (t0) cc_final: 0.7913 (t0) REVERT: A 163 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 272 SER cc_start: 0.8804 (t) cc_final: 0.8440 (m) REVERT: A 336 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7286 (tpp-160) REVERT: A 342 GLN cc_start: 0.7139 (tp40) cc_final: 0.6897 (tm-30) REVERT: A 371 SER cc_start: 0.8304 (t) cc_final: 0.8099 (t) REVERT: A 411 MET cc_start: 0.8333 (tmm) cc_final: 0.7974 (ttp) REVERT: A 424 ASN cc_start: 0.7768 (p0) cc_final: 0.7561 (p0) REVERT: A 468 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8073 (mm-40) REVERT: J 30 SER cc_start: 0.8613 (p) cc_final: 0.8286 (t) REVERT: B 45 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7987 (mtmm) REVERT: B 136 GLU cc_start: 0.7803 (mp0) cc_final: 0.7496 (mp0) REVERT: B 139 LYS cc_start: 0.8338 (mttp) cc_final: 0.8078 (mttp) REVERT: B 254 ASP cc_start: 0.7897 (m-30) cc_final: 0.7611 (m-30) REVERT: B 371 SER cc_start: 0.8364 (t) cc_final: 0.8147 (t) REVERT: B 411 MET cc_start: 0.8356 (tmm) cc_final: 0.7907 (ttp) REVERT: C 139 LYS cc_start: 0.8428 (mttp) cc_final: 0.8190 (mttp) REVERT: C 145 ASN cc_start: 0.7996 (m-40) cc_final: 0.7746 (m-40) REVERT: C 148 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7796 (tttm) REVERT: C 208 SER cc_start: 0.8707 (m) cc_final: 0.8433 (m) REVERT: C 240 GLU cc_start: 0.8175 (tp30) cc_final: 0.7950 (tp30) REVERT: C 411 MET cc_start: 0.8340 (tmm) cc_final: 0.8006 (ttp) REVERT: K 42 GLN cc_start: 0.7950 (mm110) cc_final: 0.7506 (mm110) REVERT: K 87 TYR cc_start: 0.8577 (m-80) cc_final: 0.8303 (m-80) outliers start: 4 outliers final: 0 residues processed: 376 average time/residue: 0.1125 time to fit residues: 63.6125 Evaluate side-chains 336 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 182 ASN A 325 ASN A 469 GLN B 320 ASN B 342 GLN C 320 ASN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106285 restraints weight = 22923.047| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.92 r_work: 0.3282 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16122 Z= 0.123 Angle : 0.541 7.180 21954 Z= 0.275 Chirality : 0.045 0.158 2625 Planarity : 0.004 0.037 2745 Dihedral : 5.787 40.242 2667 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.32 % Allowed : 8.49 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.52 (0.18), residues: 1983 helix: -1.45 (0.22), residues: 396 sheet: 0.35 (0.23), residues: 573 loop : -1.64 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.013 0.001 TYR C 178 PHE 0.006 0.001 PHE A 282 TRP 0.008 0.001 TRP H 112 HIS 0.002 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00283 (16077) covalent geometry : angle 0.52417 (21840) SS BOND : bond 0.00459 ( 21) SS BOND : angle 0.81705 ( 42) hydrogen bonds : bond 0.04392 ( 504) hydrogen bonds : angle 5.36570 ( 1338) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 1.50804 ( 9) link_BETA1-4 : bond 0.00578 ( 9) link_BETA1-4 : angle 2.43375 ( 27) link_NAG-ASN : bond 0.00606 ( 12) link_NAG-ASN : angle 2.47237 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 346 time to evaluate : 0.386 Fit side-chains REVERT: A 74 SER cc_start: 0.8341 (m) cc_final: 0.7862 (t) REVERT: A 182 ASN cc_start: 0.7909 (m-40) cc_final: 0.7693 (m110) REVERT: A 272 SER cc_start: 0.8793 (t) cc_final: 0.8424 (m) REVERT: A 336 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7443 (tpp-160) REVERT: A 371 SER cc_start: 0.8262 (t) cc_final: 0.8005 (t) REVERT: A 468 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8293 (mp10) REVERT: H 76 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8237 (mtmm) REVERT: J 30 SER cc_start: 0.8537 (p) cc_final: 0.8230 (t) REVERT: L 42 GLN cc_start: 0.8112 (tp40) cc_final: 0.7738 (mp10) REVERT: B 45 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7965 (mtmm) REVERT: B 254 ASP cc_start: 0.7583 (m-30) cc_final: 0.7331 (m-30) REVERT: B 371 SER cc_start: 0.8307 (t) cc_final: 0.8052 (t) REVERT: B 411 MET cc_start: 0.8381 (tmm) cc_final: 0.8080 (ttp) REVERT: B 468 GLN cc_start: 0.8270 (mp10) cc_final: 0.7963 (mp10) REVERT: C 145 ASN cc_start: 0.8019 (m-40) cc_final: 0.7726 (m-40) REVERT: C 200 ASP cc_start: 0.8069 (m-30) cc_final: 0.7821 (m-30) REVERT: C 208 SER cc_start: 0.8596 (m) cc_final: 0.8358 (m) REVERT: C 350 ASN cc_start: 0.8369 (t0) cc_final: 0.8033 (m-40) REVERT: C 468 GLN cc_start: 0.8305 (mp10) cc_final: 0.7698 (mp10) outliers start: 23 outliers final: 19 residues processed: 355 average time/residue: 0.1085 time to fit residues: 58.3635 Evaluate side-chains 345 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 326 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 90 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 342 GLN A 469 GLN B 320 ASN B 469 GLN C 70 GLN C 229 GLN N 90 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111343 restraints weight = 22761.313| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3275 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16122 Z= 0.150 Angle : 0.537 5.766 21954 Z= 0.273 Chirality : 0.045 0.156 2625 Planarity : 0.004 0.033 2745 Dihedral : 5.260 34.054 2667 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.98 % Allowed : 9.64 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.04 (0.19), residues: 1983 helix: -0.28 (0.25), residues: 396 sheet: 0.52 (0.24), residues: 558 loop : -1.59 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 91 TYR 0.015 0.001 TYR A 275 PHE 0.009 0.001 PHE H 29 TRP 0.009 0.002 TRP H 47 HIS 0.015 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00356 (16077) covalent geometry : angle 0.52154 (21840) SS BOND : bond 0.00401 ( 21) SS BOND : angle 1.02955 ( 42) hydrogen bonds : bond 0.03587 ( 504) hydrogen bonds : angle 4.72848 ( 1338) link_ALPHA1-3 : bond 0.01197 ( 3) link_ALPHA1-3 : angle 1.55653 ( 9) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 2.37760 ( 27) link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 2.19882 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 355 time to evaluate : 0.384 Fit side-chains REVERT: A 74 SER cc_start: 0.8463 (m) cc_final: 0.7979 (t) REVERT: A 163 GLU cc_start: 0.7376 (tt0) cc_final: 0.7062 (mt-10) REVERT: A 182 ASN cc_start: 0.8015 (m-40) cc_final: 0.7730 (m-40) REVERT: A 272 SER cc_start: 0.8812 (t) cc_final: 0.8471 (m) REVERT: A 285 LEU cc_start: 0.8905 (mt) cc_final: 0.8684 (mt) REVERT: A 336 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7501 (tpp-160) REVERT: A 371 SER cc_start: 0.8284 (t) cc_final: 0.8054 (t) REVERT: A 468 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8336 (mp10) REVERT: H 76 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8249 (mtmm) REVERT: J 30 SER cc_start: 0.8543 (p) cc_final: 0.8266 (t) REVERT: L 42 GLN cc_start: 0.8192 (tp40) cc_final: 0.7853 (mp10) REVERT: B 210 LEU cc_start: 0.8011 (tp) cc_final: 0.7774 (tt) REVERT: B 254 ASP cc_start: 0.7538 (m-30) cc_final: 0.7268 (m-30) REVERT: B 354 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 371 SER cc_start: 0.8324 (t) cc_final: 0.8093 (t) REVERT: B 411 MET cc_start: 0.8363 (tmm) cc_final: 0.7910 (tmm) REVERT: B 468 GLN cc_start: 0.8265 (mp10) cc_final: 0.8056 (mp10) REVERT: C 182 ASN cc_start: 0.8002 (m-40) cc_final: 0.7795 (m-40) REVERT: C 208 SER cc_start: 0.8550 (m) cc_final: 0.8263 (p) REVERT: C 337 SER cc_start: 0.8086 (t) cc_final: 0.7693 (p) REVERT: C 411 MET cc_start: 0.8447 (tmm) cc_final: 0.8135 (ttp) REVERT: C 462 SER cc_start: 0.8064 (m) cc_final: 0.7810 (m) REVERT: C 468 GLN cc_start: 0.8395 (mp10) cc_final: 0.7990 (mp10) outliers start: 52 outliers final: 38 residues processed: 371 average time/residue: 0.1138 time to fit residues: 63.3793 Evaluate side-chains 372 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 101 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 342 GLN A 469 GLN B 51 ASN B 70 GLN B 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112215 restraints weight = 22770.092| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.01 r_work: 0.3274 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16122 Z= 0.102 Angle : 0.490 5.605 21954 Z= 0.250 Chirality : 0.044 0.152 2625 Planarity : 0.003 0.033 2745 Dihedral : 4.858 29.001 2667 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.75 % Allowed : 11.19 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.77 (0.19), residues: 1983 helix: 0.28 (0.26), residues: 396 sheet: 0.56 (0.24), residues: 558 loop : -1.49 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 91 TYR 0.008 0.001 TYR A 275 PHE 0.009 0.001 PHE N 71 TRP 0.007 0.001 TRP H 112 HIS 0.002 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00236 (16077) covalent geometry : angle 0.47777 (21840) SS BOND : bond 0.00330 ( 21) SS BOND : angle 0.77306 ( 42) hydrogen bonds : bond 0.03038 ( 504) hydrogen bonds : angle 4.49210 ( 1338) link_ALPHA1-3 : bond 0.01225 ( 3) link_ALPHA1-3 : angle 1.49643 ( 9) link_BETA1-4 : bond 0.00512 ( 9) link_BETA1-4 : angle 2.03637 ( 27) link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 1.87737 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 0.397 Fit side-chains REVERT: A 74 SER cc_start: 0.8402 (m) cc_final: 0.7926 (t) REVERT: A 272 SER cc_start: 0.8796 (t) cc_final: 0.8461 (m) REVERT: A 285 LEU cc_start: 0.8920 (mt) cc_final: 0.8711 (mt) REVERT: A 336 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7533 (tpp-160) REVERT: A 371 SER cc_start: 0.8264 (t) cc_final: 0.8047 (t) REVERT: H 76 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8234 (mtmm) REVERT: H 95 TYR cc_start: 0.7992 (m-80) cc_final: 0.7792 (m-80) REVERT: J 30 SER cc_start: 0.8576 (p) cc_final: 0.8286 (t) REVERT: L 42 GLN cc_start: 0.8242 (tp40) cc_final: 0.7882 (mp10) REVERT: B 45 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7962 (mtmm) REVERT: B 254 ASP cc_start: 0.7539 (m-30) cc_final: 0.7257 (m-30) REVERT: B 354 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: B 371 SER cc_start: 0.8322 (t) cc_final: 0.8090 (t) REVERT: B 411 MET cc_start: 0.8397 (tmm) cc_final: 0.7926 (tmm) REVERT: B 468 GLN cc_start: 0.8301 (mp10) cc_final: 0.8073 (mp10) REVERT: C 208 SER cc_start: 0.8523 (m) cc_final: 0.8243 (p) REVERT: C 337 SER cc_start: 0.8168 (t) cc_final: 0.7770 (p) REVERT: C 462 SER cc_start: 0.8084 (m) cc_final: 0.7846 (m) REVERT: C 468 GLN cc_start: 0.8416 (mp10) cc_final: 0.8211 (mp10) outliers start: 48 outliers final: 30 residues processed: 358 average time/residue: 0.1121 time to fit residues: 60.1991 Evaluate side-chains 363 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 332 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 0.0470 chunk 170 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 325 ASN A 468 GLN A 469 GLN M 114 GLN B 51 ASN B 320 ASN B 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111737 restraints weight = 22673.361| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.88 r_work: 0.3280 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16122 Z= 0.107 Angle : 0.487 6.208 21954 Z= 0.249 Chirality : 0.044 0.158 2625 Planarity : 0.003 0.032 2745 Dihedral : 4.495 22.985 2667 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 11.53 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.61 (0.19), residues: 1983 helix: 0.60 (0.27), residues: 396 sheet: 0.61 (0.24), residues: 558 loop : -1.43 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.012 0.001 TYR A 178 PHE 0.006 0.001 PHE A 301 TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00253 (16077) covalent geometry : angle 0.47602 (21840) SS BOND : bond 0.00311 ( 21) SS BOND : angle 0.72308 ( 42) hydrogen bonds : bond 0.02938 ( 504) hydrogen bonds : angle 4.31259 ( 1338) link_ALPHA1-3 : bond 0.01062 ( 3) link_ALPHA1-3 : angle 1.48104 ( 9) link_BETA1-4 : bond 0.00458 ( 9) link_BETA1-4 : angle 1.92404 ( 27) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 1.81764 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.578 Fit side-chains REVERT: A 68 MET cc_start: 0.8521 (ptm) cc_final: 0.8318 (ptp) REVERT: A 74 SER cc_start: 0.8400 (m) cc_final: 0.7958 (t) REVERT: A 208 SER cc_start: 0.8584 (m) cc_final: 0.8267 (p) REVERT: A 272 SER cc_start: 0.8784 (t) cc_final: 0.8449 (m) REVERT: A 285 LEU cc_start: 0.8908 (mt) cc_final: 0.8691 (mt) REVERT: A 336 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7518 (tpp-160) REVERT: A 371 SER cc_start: 0.8270 (t) cc_final: 0.8043 (t) REVERT: H 76 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8220 (mtmm) REVERT: J 30 SER cc_start: 0.8559 (p) cc_final: 0.8276 (t) REVERT: L 42 GLN cc_start: 0.8231 (tp40) cc_final: 0.7875 (mp10) REVERT: B 45 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7935 (mtmm) REVERT: B 210 LEU cc_start: 0.8024 (tp) cc_final: 0.7783 (tt) REVERT: B 254 ASP cc_start: 0.7513 (m-30) cc_final: 0.7190 (m-30) REVERT: B 354 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: B 371 SER cc_start: 0.8312 (t) cc_final: 0.8086 (t) REVERT: B 411 MET cc_start: 0.8384 (tmm) cc_final: 0.7909 (tmm) REVERT: B 468 GLN cc_start: 0.8289 (mp10) cc_final: 0.8028 (mp10) REVERT: C 136 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: C 208 SER cc_start: 0.8509 (m) cc_final: 0.8271 (p) REVERT: C 337 SER cc_start: 0.8217 (t) cc_final: 0.7850 (p) REVERT: C 462 SER cc_start: 0.8089 (m) cc_final: 0.7853 (m) REVERT: C 468 GLN cc_start: 0.8381 (mp10) cc_final: 0.8142 (mp10) outliers start: 50 outliers final: 34 residues processed: 353 average time/residue: 0.1118 time to fit residues: 58.9636 Evaluate side-chains 360 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 114 GLN Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 431 LYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 100 ASN A 140 ASN A 325 ASN A 342 GLN A 469 GLN B 51 ASN B 320 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102180 restraints weight = 22754.028| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.90 r_work: 0.3206 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16122 Z= 0.247 Angle : 0.631 7.494 21954 Z= 0.319 Chirality : 0.049 0.164 2625 Planarity : 0.004 0.044 2745 Dihedral : 5.040 27.894 2667 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.93 % Allowed : 12.34 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.69 (0.19), residues: 1983 helix: 0.58 (0.27), residues: 396 sheet: 0.52 (0.22), residues: 594 loop : -1.54 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 91 TYR 0.022 0.002 TYR A 275 PHE 0.014 0.002 PHE A 301 TRP 0.010 0.002 TRP H 36 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00595 (16077) covalent geometry : angle 0.61431 (21840) SS BOND : bond 0.00572 ( 21) SS BOND : angle 1.26902 ( 42) hydrogen bonds : bond 0.04073 ( 504) hydrogen bonds : angle 4.53772 ( 1338) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.48205 ( 9) link_BETA1-4 : bond 0.00318 ( 9) link_BETA1-4 : angle 2.67485 ( 27) link_NAG-ASN : bond 0.00472 ( 12) link_NAG-ASN : angle 2.39183 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 0.593 Fit side-chains REVERT: A 68 MET cc_start: 0.8569 (ptm) cc_final: 0.8364 (ptp) REVERT: A 74 SER cc_start: 0.8616 (m) cc_final: 0.8196 (t) REVERT: A 145 ASN cc_start: 0.8285 (m-40) cc_final: 0.8036 (m-40) REVERT: A 238 ASN cc_start: 0.8121 (t0) cc_final: 0.7921 (t0) REVERT: A 272 SER cc_start: 0.8852 (t) cc_final: 0.8533 (m) REVERT: A 285 LEU cc_start: 0.8951 (mt) cc_final: 0.8738 (mt) REVERT: A 336 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7555 (tpp-160) REVERT: A 371 SER cc_start: 0.8376 (t) cc_final: 0.8157 (t) REVERT: H 76 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8235 (mtmm) REVERT: M 30 SER cc_start: 0.8557 (p) cc_final: 0.8290 (t) REVERT: L 42 GLN cc_start: 0.8280 (tp40) cc_final: 0.7879 (mp10) REVERT: B 145 ASN cc_start: 0.8371 (m-40) cc_final: 0.8167 (m-40) REVERT: B 254 ASP cc_start: 0.7569 (m-30) cc_final: 0.7299 (m-30) REVERT: B 354 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: B 371 SER cc_start: 0.8408 (t) cc_final: 0.8180 (t) REVERT: B 391 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 411 MET cc_start: 0.8353 (tmm) cc_final: 0.8024 (tmm) REVERT: B 467 LEU cc_start: 0.8743 (mt) cc_final: 0.8537 (mp) REVERT: B 468 GLN cc_start: 0.8411 (mp10) cc_final: 0.8126 (mp10) REVERT: C 136 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: C 145 ASN cc_start: 0.8152 (m-40) cc_final: 0.7844 (m-40) REVERT: C 208 SER cc_start: 0.8563 (m) cc_final: 0.8255 (p) REVERT: C 337 SER cc_start: 0.8312 (t) cc_final: 0.8028 (p) REVERT: C 411 MET cc_start: 0.8371 (tmm) cc_final: 0.7869 (ttp) REVERT: C 468 GLN cc_start: 0.8517 (mp10) cc_final: 0.8206 (mp10) REVERT: N 67 SER cc_start: 0.8251 (p) cc_final: 0.8044 (t) outliers start: 51 outliers final: 40 residues processed: 387 average time/residue: 0.1073 time to fit residues: 63.2322 Evaluate side-chains 394 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 182 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 469 GLN B 51 ASN B 290 GLN B 305 ASN C 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104253 restraints weight = 22734.987| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.90 r_work: 0.3251 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16122 Z= 0.121 Angle : 0.514 5.540 21954 Z= 0.264 Chirality : 0.045 0.169 2625 Planarity : 0.003 0.037 2745 Dihedral : 4.664 27.465 2667 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.87 % Allowed : 13.77 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.57 (0.19), residues: 1983 helix: 0.76 (0.27), residues: 399 sheet: 0.51 (0.23), residues: 588 loop : -1.44 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.016 0.001 TYR B 248 PHE 0.010 0.001 PHE N 71 TRP 0.011 0.001 TRP M 112 HIS 0.003 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00284 (16077) covalent geometry : angle 0.50319 (21840) SS BOND : bond 0.00316 ( 21) SS BOND : angle 0.75131 ( 42) hydrogen bonds : bond 0.03154 ( 504) hydrogen bonds : angle 4.34692 ( 1338) link_ALPHA1-3 : bond 0.01021 ( 3) link_ALPHA1-3 : angle 1.19570 ( 9) link_BETA1-4 : bond 0.00583 ( 9) link_BETA1-4 : angle 2.06515 ( 27) link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 1.87133 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 0.573 Fit side-chains REVERT: A 68 MET cc_start: 0.8499 (ptm) cc_final: 0.8245 (ptp) REVERT: A 74 SER cc_start: 0.8585 (m) cc_final: 0.8181 (t) REVERT: A 208 SER cc_start: 0.8600 (m) cc_final: 0.8304 (p) REVERT: A 238 ASN cc_start: 0.8068 (t0) cc_final: 0.7853 (t0) REVERT: A 272 SER cc_start: 0.8830 (t) cc_final: 0.8524 (m) REVERT: A 285 LEU cc_start: 0.8930 (mt) cc_final: 0.8723 (mt) REVERT: A 336 ARG cc_start: 0.7769 (tpp-160) cc_final: 0.7557 (tpp-160) REVERT: H 76 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8213 (mtmm) REVERT: L 42 GLN cc_start: 0.8301 (tp40) cc_final: 0.7904 (mp10) REVERT: B 254 ASP cc_start: 0.7552 (m-30) cc_final: 0.7280 (m-30) REVERT: B 354 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: B 371 SER cc_start: 0.8405 (t) cc_final: 0.8174 (t) REVERT: B 375 ARG cc_start: 0.7995 (mpt180) cc_final: 0.7718 (mtt90) REVERT: B 411 MET cc_start: 0.8373 (tmm) cc_final: 0.7944 (tmm) REVERT: B 440 SER cc_start: 0.8958 (m) cc_final: 0.8555 (p) REVERT: B 467 LEU cc_start: 0.8775 (mt) cc_final: 0.8542 (mp) REVERT: B 468 GLN cc_start: 0.8295 (mp10) cc_final: 0.7953 (mp10) REVERT: C 136 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: C 145 ASN cc_start: 0.8054 (m-40) cc_final: 0.7698 (m-40) REVERT: C 208 SER cc_start: 0.8541 (m) cc_final: 0.8298 (p) REVERT: C 337 SER cc_start: 0.8253 (t) cc_final: 0.7941 (p) REVERT: C 411 MET cc_start: 0.8368 (tmm) cc_final: 0.7765 (ttp) REVERT: C 468 GLN cc_start: 0.8403 (mp10) cc_final: 0.8083 (mp10) outliers start: 50 outliers final: 36 residues processed: 375 average time/residue: 0.1063 time to fit residues: 60.1143 Evaluate side-chains 395 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 357 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 178 optimal weight: 0.0770 chunk 104 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 342 GLN A 469 GLN B 51 ASN B 320 ASN B 403 GLN C 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110990 restraints weight = 22816.947| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.88 r_work: 0.3265 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16122 Z= 0.102 Angle : 0.495 5.358 21954 Z= 0.256 Chirality : 0.044 0.164 2625 Planarity : 0.003 0.056 2745 Dihedral : 4.369 23.547 2667 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 15.03 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.47 (0.19), residues: 1983 helix: 0.92 (0.27), residues: 399 sheet: 0.61 (0.23), residues: 558 loop : -1.39 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.015 0.001 TYR B 248 PHE 0.009 0.001 PHE N 71 TRP 0.008 0.001 TRP M 112 HIS 0.002 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00238 (16077) covalent geometry : angle 0.48507 (21840) SS BOND : bond 0.00277 ( 21) SS BOND : angle 0.62831 ( 42) hydrogen bonds : bond 0.02900 ( 504) hydrogen bonds : angle 4.22247 ( 1338) link_ALPHA1-3 : bond 0.00891 ( 3) link_ALPHA1-3 : angle 1.30633 ( 9) link_BETA1-4 : bond 0.00540 ( 9) link_BETA1-4 : angle 1.90615 ( 27) link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 1.73728 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 343 time to evaluate : 0.422 Fit side-chains REVERT: A 68 MET cc_start: 0.8475 (ptm) cc_final: 0.8224 (ptp) REVERT: A 74 SER cc_start: 0.8520 (m) cc_final: 0.8142 (t) REVERT: A 136 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7585 (mm-30) REVERT: A 208 SER cc_start: 0.8578 (m) cc_final: 0.8315 (p) REVERT: A 238 ASN cc_start: 0.8062 (t0) cc_final: 0.7830 (t0) REVERT: A 272 SER cc_start: 0.8772 (t) cc_final: 0.8317 (m) REVERT: A 285 LEU cc_start: 0.8940 (mt) cc_final: 0.8737 (mt) REVERT: A 336 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7511 (tpp-160) REVERT: H 76 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8214 (mtmm) REVERT: J 76 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7950 (mtmm) REVERT: L 42 GLN cc_start: 0.8287 (tp40) cc_final: 0.7861 (mp10) REVERT: B 254 ASP cc_start: 0.7499 (m-30) cc_final: 0.7194 (m-30) REVERT: B 354 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 371 SER cc_start: 0.8391 (t) cc_final: 0.8163 (t) REVERT: B 375 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7667 (mtt90) REVERT: B 440 SER cc_start: 0.8939 (m) cc_final: 0.8536 (p) REVERT: B 467 LEU cc_start: 0.8768 (mt) cc_final: 0.8523 (mp) REVERT: B 468 GLN cc_start: 0.8287 (mp10) cc_final: 0.8008 (mp10) REVERT: C 145 ASN cc_start: 0.8010 (m-40) cc_final: 0.7662 (m-40) REVERT: C 208 SER cc_start: 0.8520 (m) cc_final: 0.8307 (p) REVERT: C 337 SER cc_start: 0.8259 (t) cc_final: 0.7950 (p) REVERT: C 468 GLN cc_start: 0.8372 (mp10) cc_final: 0.8056 (mp10) outliers start: 39 outliers final: 33 residues processed: 357 average time/residue: 0.1067 time to fit residues: 57.0831 Evaluate side-chains 376 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 194 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 104 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 469 GLN B 51 ASN B 320 ASN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110939 restraints weight = 22782.988| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.86 r_work: 0.3266 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16122 Z= 0.109 Angle : 0.500 5.480 21954 Z= 0.257 Chirality : 0.044 0.163 2625 Planarity : 0.004 0.071 2745 Dihedral : 4.271 22.046 2667 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.58 % Allowed : 14.80 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.42 (0.19), residues: 1983 helix: 1.00 (0.27), residues: 399 sheet: 0.63 (0.23), residues: 558 loop : -1.36 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.016 0.001 TYR B 248 PHE 0.009 0.001 PHE N 71 TRP 0.009 0.001 TRP M 112 HIS 0.002 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00258 (16077) covalent geometry : angle 0.48984 (21840) SS BOND : bond 0.00285 ( 21) SS BOND : angle 0.67678 ( 42) hydrogen bonds : bond 0.02866 ( 504) hydrogen bonds : angle 4.17092 ( 1338) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 1.30204 ( 9) link_BETA1-4 : bond 0.00517 ( 9) link_BETA1-4 : angle 1.87247 ( 27) link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.75899 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 344 time to evaluate : 0.453 Fit side-chains REVERT: A 68 MET cc_start: 0.8481 (ptm) cc_final: 0.8260 (ptp) REVERT: A 74 SER cc_start: 0.8503 (m) cc_final: 0.8168 (t) REVERT: A 136 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7591 (mm-30) REVERT: A 208 SER cc_start: 0.8575 (m) cc_final: 0.8322 (p) REVERT: A 238 ASN cc_start: 0.8058 (t0) cc_final: 0.7820 (t0) REVERT: A 285 LEU cc_start: 0.8941 (mt) cc_final: 0.8727 (mt) REVERT: A 336 ARG cc_start: 0.7737 (tpp-160) cc_final: 0.7501 (tpp-160) REVERT: H 76 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8222 (mtmm) REVERT: J 30 SER cc_start: 0.8570 (p) cc_final: 0.8286 (t) REVERT: J 76 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7951 (mtmm) REVERT: L 42 GLN cc_start: 0.8302 (tp40) cc_final: 0.7832 (mp10) REVERT: B 254 ASP cc_start: 0.7503 (m-30) cc_final: 0.7171 (m-30) REVERT: B 354 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: B 371 SER cc_start: 0.8403 (t) cc_final: 0.8193 (t) REVERT: B 411 MET cc_start: 0.8378 (tmm) cc_final: 0.8035 (tmm) REVERT: B 440 SER cc_start: 0.8955 (m) cc_final: 0.8550 (p) REVERT: B 467 LEU cc_start: 0.8781 (mt) cc_final: 0.8542 (mp) REVERT: B 468 GLN cc_start: 0.8256 (mp10) cc_final: 0.7936 (mp10) REVERT: C 168 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (m) REVERT: C 337 SER cc_start: 0.8251 (t) cc_final: 0.7943 (p) REVERT: C 468 GLN cc_start: 0.8348 (mp10) cc_final: 0.8066 (mp10) REVERT: N 42 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7809 (mm-40) outliers start: 45 outliers final: 39 residues processed: 356 average time/residue: 0.1062 time to fit residues: 56.7572 Evaluate side-chains 382 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 340 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 74 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 196 optimal weight: 0.8980 chunk 153 optimal weight: 0.3980 chunk 94 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 290 GLN A 342 GLN A 469 GLN B 51 ASN B 320 ASN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 320 ASN C 469 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111575 restraints weight = 22655.335| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.87 r_work: 0.3273 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16122 Z= 0.104 Angle : 0.494 5.967 21954 Z= 0.255 Chirality : 0.044 0.161 2625 Planarity : 0.004 0.066 2745 Dihedral : 4.184 22.205 2667 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 15.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.39 (0.19), residues: 1983 helix: 1.04 (0.27), residues: 399 sheet: 0.64 (0.23), residues: 558 loop : -1.35 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.015 0.001 TYR B 248 PHE 0.008 0.001 PHE N 71 TRP 0.009 0.001 TRP M 112 HIS 0.002 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00245 (16077) covalent geometry : angle 0.48463 (21840) SS BOND : bond 0.00265 ( 21) SS BOND : angle 0.63448 ( 42) hydrogen bonds : bond 0.02771 ( 504) hydrogen bonds : angle 4.11613 ( 1338) link_ALPHA1-3 : bond 0.00834 ( 3) link_ALPHA1-3 : angle 1.30292 ( 9) link_BETA1-4 : bond 0.00528 ( 9) link_BETA1-4 : angle 1.80255 ( 27) link_NAG-ASN : bond 0.00283 ( 12) link_NAG-ASN : angle 1.74481 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.456 Fit side-chains REVERT: A 68 MET cc_start: 0.8458 (ptm) cc_final: 0.8217 (ptp) REVERT: A 74 SER cc_start: 0.8469 (m) cc_final: 0.8071 (t) REVERT: A 136 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7614 (mm-30) REVERT: A 208 SER cc_start: 0.8571 (m) cc_final: 0.8327 (p) REVERT: A 238 ASN cc_start: 0.8067 (t0) cc_final: 0.7828 (t0) REVERT: A 285 LEU cc_start: 0.8940 (mt) cc_final: 0.8728 (mt) REVERT: A 336 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.7523 (tpp-160) REVERT: A 361 GLU cc_start: 0.7132 (mp0) cc_final: 0.6892 (pm20) REVERT: H 76 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8223 (mtmm) REVERT: J 30 SER cc_start: 0.8568 (p) cc_final: 0.8277 (t) REVERT: J 76 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7917 (mtmm) REVERT: L 42 GLN cc_start: 0.8312 (tp40) cc_final: 0.7829 (mp10) REVERT: B 68 MET cc_start: 0.7413 (ttm) cc_final: 0.7206 (ttm) REVERT: B 254 ASP cc_start: 0.7470 (m-30) cc_final: 0.7135 (m-30) REVERT: B 371 SER cc_start: 0.8407 (t) cc_final: 0.8044 (p) REVERT: B 411 MET cc_start: 0.8384 (tmm) cc_final: 0.8008 (tmm) REVERT: B 440 SER cc_start: 0.8949 (m) cc_final: 0.8548 (p) REVERT: B 468 GLN cc_start: 0.8237 (mp10) cc_final: 0.7955 (mp10) REVERT: C 168 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7815 (m) REVERT: C 337 SER cc_start: 0.8228 (t) cc_final: 0.7914 (p) REVERT: C 468 GLN cc_start: 0.8326 (mp10) cc_final: 0.8059 (mp10) REVERT: N 42 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7857 (mm-40) outliers start: 43 outliers final: 39 residues processed: 355 average time/residue: 0.1015 time to fit residues: 54.1648 Evaluate side-chains 382 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 290 GLN A 342 GLN A 469 GLN B 51 ASN B 320 ASN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104280 restraints weight = 22731.698| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.89 r_work: 0.3249 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16122 Z= 0.143 Angle : 0.537 10.247 21954 Z= 0.273 Chirality : 0.045 0.163 2625 Planarity : 0.004 0.067 2745 Dihedral : 4.300 22.556 2667 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.70 % Allowed : 15.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.40 (0.19), residues: 1983 helix: 1.00 (0.27), residues: 399 sheet: 0.61 (0.22), residues: 594 loop : -1.39 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.020 0.001 TYR C 178 PHE 0.008 0.001 PHE N 71 TRP 0.010 0.001 TRP M 112 HIS 0.003 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00346 (16077) covalent geometry : angle 0.52568 (21840) SS BOND : bond 0.00359 ( 21) SS BOND : angle 0.83472 ( 42) hydrogen bonds : bond 0.03126 ( 504) hydrogen bonds : angle 4.16807 ( 1338) link_ALPHA1-3 : bond 0.00819 ( 3) link_ALPHA1-3 : angle 1.35465 ( 9) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 2.04271 ( 27) link_NAG-ASN : bond 0.00282 ( 12) link_NAG-ASN : angle 1.93873 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.21 seconds wall clock time: 59 minutes 15.47 seconds (3555.47 seconds total)