Starting phenix.real_space_refine on Mon Aug 25 21:12:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dof_47082/08_2025/9dof_47082.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 138 5.16 5 C 9723 2.51 5 N 2628 2.21 5 O 2862 1.98 5 H 15408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30759 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7643 Classifications: {'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 474} Chain: "B" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7644 Classifications: {'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 474} Chain: "C" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7643 Classifications: {'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 474} Chain: "D" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2609 Classifications: {'peptide': 166} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2611 Classifications: {'peptide': 166} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 158} Chain: "F" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2609 Classifications: {'peptide': 166} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 159} Time building chain proxies: 5.37, per 1000 atoms: 0.17 Number of scatterers: 30759 At special positions: 0 Unit cell: (163.59, 177.12, 147.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 O 2862 8.00 N 2628 7.00 C 9723 6.00 H 15408 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.11 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.04 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.02 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 285 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 68 " distance=2.03 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 788.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 33 sheets defined 25.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.716A pdb=" N PHE A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 396 through 415 Processing helix chain 'A' and resid 426 through 447 removed outlier: 4.108A pdb=" N THR A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.662A pdb=" N LEU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.760A pdb=" N GLN B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 87' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.853A pdb=" N VAL B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.508A pdb=" N LEU B 216 " --> pdb=" O TRP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.675A pdb=" N THR B 265 " --> pdb=" O HIS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 396 through 415 Processing helix chain 'B' and resid 426 through 440 removed outlier: 4.198A pdb=" N THR B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 446 Processing helix chain 'B' and resid 452 through 469 removed outlier: 3.517A pdb=" N LYS B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 495 removed outlier: 3.716A pdb=" N LEU B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.606A pdb=" N LEU C 216 " --> pdb=" O TRP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.859A pdb=" N THR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 237 " --> pdb=" O LYS C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 237' Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.558A pdb=" N SER C 274 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 415 Processing helix chain 'C' and resid 427 through 446 removed outlier: 6.434A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 Processing helix chain 'C' and resid 472 through 494 removed outlier: 4.024A pdb=" N VAL C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 removed outlier: 4.167A pdb=" N HIS D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 145 Processing helix chain 'D' and resid 147 through 166 Proline residue: D 163 - end of helix removed outlier: 4.099A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 4.681A pdb=" N HIS E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 145 Processing helix chain 'E' and resid 147 through 166 Proline residue: E 163 - end of helix removed outlier: 3.743A pdb=" N THR E 166 " --> pdb=" O ALA E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 108 through 130 removed outlier: 3.539A pdb=" N HIS F 130 " --> pdb=" O TRP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 145 removed outlier: 4.112A pdb=" N THR F 134 " --> pdb=" O HIS F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 166 Proline residue: F 163 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.422A pdb=" N SER A 29 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A 45 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 138 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 25 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.903A pdb=" N ALA A 205 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 270 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 268 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 72 removed outlier: 3.779A pdb=" N THR A 120 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 66 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A 72 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 171 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.921A pdb=" N SER A 300 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS A 333 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 358 " --> pdb=" O CYS A 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 307 through 310 removed outlier: 4.696A pdb=" N VAL A 308 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN A 325 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 310 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 323 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 13 removed outlier: 7.061A pdb=" N ASN B 8 " --> pdb=" O CYS B 30 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR B 32 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N MET B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 12 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER B 29 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU B 45 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 43 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 142 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU B 45 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 140 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 47 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 25 Processing sheet with id=AB4, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.684A pdb=" N ALA B 54 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY B 127 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B 268 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 73 removed outlier: 4.857A pdb=" N LEU B 65 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 120 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASN B 67 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET B 118 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 171 through 175 Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AB8, first strand: chain 'B' and resid 307 through 308 removed outlier: 3.690A pdb=" N VAL B 321 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 313 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC1, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 12 removed outlier: 7.290A pdb=" N THR C 138 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.966A pdb=" N ARG C 288 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 182 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 173 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222 removed outlier: 5.945A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 205 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 268 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AC6, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AC7, first strand: chain 'C' and resid 307 through 308 removed outlier: 3.568A pdb=" N ARG C 350 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 333 through 334 removed outlier: 3.674A pdb=" N VAL C 358 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AD1, first strand: chain 'D' and resid 2 through 6 removed outlier: 8.061A pdb=" N THR D 76 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET D 12 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 23 through 27 Processing sheet with id=AD3, first strand: chain 'E' and resid 4 through 6 removed outlier: 7.507A pdb=" N ASP E 47 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 23 through 27 Processing sheet with id=AD5, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.314A pdb=" N GLY F 78 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 23 through 24 635 hydrogen bonds defined for protein. 1704 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: 6.10 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.07: 15406 1.07 - 1.31: 2525 1.31 - 1.55: 12888 1.55 - 1.78: 50 1.78 - 2.02: 208 Bond restraints: 31077 Sorted by residual: bond pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 1.808 2.020 -0.212 3.30e-02 9.18e+02 4.11e+01 bond pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 1.808 1.604 0.204 3.30e-02 9.18e+02 3.81e+01 bond pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sigma weight residual 1.530 1.463 0.067 1.93e-02 2.68e+03 1.21e+01 bond pdb=" CB CYS B 116 " pdb=" SG CYS B 116 " ideal model delta sigma weight residual 1.808 1.695 0.113 3.30e-02 9.18e+02 1.17e+01 bond pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " ideal model delta sigma weight residual 1.808 1.710 0.098 3.30e-02 9.18e+02 8.81e+00 ... (remaining 31072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.64: 56312 7.64 - 15.29: 17 15.29 - 22.93: 8 22.93 - 30.57: 0 30.57 - 38.22: 1 Bond angle restraints: 56338 Sorted by residual: angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 152.62 -38.22 2.30e+00 1.89e-01 2.76e+02 angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 135.83 -21.43 2.30e+00 1.89e-01 8.68e+01 angle pdb=" N CYS A 116 " pdb=" CA CYS A 116 " pdb=" C CYS A 116 " ideal model delta sigma weight residual 107.73 121.71 -13.98 1.61e+00 3.86e-01 7.54e+01 angle pdb=" CA CYS B 116 " pdb=" CB CYS B 116 " pdb=" SG CYS B 116 " ideal model delta sigma weight residual 114.40 132.08 -17.68 2.30e+00 1.89e-01 5.91e+01 angle pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " pdb=" HB3 CYS A 92 " ideal model delta sigma weight residual 108.00 85.45 22.55 3.00e+00 1.11e-01 5.65e+01 ... (remaining 56333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12836 17.87 - 35.74: 1259 35.74 - 53.61: 352 53.61 - 71.49: 114 71.49 - 89.36: 10 Dihedral angle restraints: 14571 sinusoidal: 8054 harmonic: 6517 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 3.07 -89.07 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA THR F 105 " pdb=" C THR F 105 " pdb=" N ARG F 106 " pdb=" CA ARG F 106 " ideal model delta harmonic sigma weight residual 180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual 93.00 163.88 -70.88 1 1.00e+01 1.00e-02 6.46e+01 ... (remaining 14568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2227 0.088 - 0.177: 187 0.177 - 0.265: 2 0.265 - 0.353: 0 0.353 - 0.441: 2 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA CYS A 92 " pdb=" N CYS A 92 " pdb=" C CYS A 92 " pdb=" CB CYS A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB VAL A 324 " pdb=" CA VAL A 324 " pdb=" CG1 VAL A 324 " pdb=" CG2 VAL A 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2415 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 91 " 0.034 2.00e-02 2.50e+03 6.73e-02 4.52e+01 pdb=" C ARG E 91 " -0.116 2.00e-02 2.50e+03 pdb=" O ARG E 91 " 0.045 2.00e-02 2.50e+03 pdb=" N SER E 92 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 91 " -0.033 2.00e-02 2.50e+03 6.66e-02 4.44e+01 pdb=" C ARG D 91 " 0.115 2.00e-02 2.50e+03 pdb=" O ARG D 91 " -0.044 2.00e-02 2.50e+03 pdb=" N SER D 92 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 91 " 0.033 2.00e-02 2.50e+03 6.64e-02 4.41e+01 pdb=" C ARG F 91 " -0.115 2.00e-02 2.50e+03 pdb=" O ARG F 91 " 0.044 2.00e-02 2.50e+03 pdb=" N SER F 92 " 0.037 2.00e-02 2.50e+03 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2841 2.22 - 2.82: 65556 2.82 - 3.41: 78215 3.41 - 4.01: 100718 4.01 - 4.60: 152549 Nonbonded interactions: 399879 Sorted by model distance: nonbonded pdb=" OE1 GLN C 211 " pdb=" H GLN C 211 " model vdw 1.628 2.450 nonbonded pdb=" OE1 GLN B 211 " pdb=" H GLN B 211 " model vdw 1.629 2.450 nonbonded pdb=" OE1 GLU A 79 " pdb=" H GLU A 79 " model vdw 1.632 2.450 nonbonded pdb=" OG SER C 16 " pdb=" H TRP C 20 " model vdw 1.646 2.450 nonbonded pdb=" O GLY B 228 " pdb=" HE1 TRP B 231 " model vdw 1.647 2.450 ... (remaining 399874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 95 through 495)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 35 through 67 or (resid 68 and (name N or name CA or name C or name O o \ r name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 69 \ through 166)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 26.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.005 0.212 15695 Z= 0.231 Angle : 0.939 38.217 21250 Z= 0.490 Chirality : 0.049 0.441 2418 Planarity : 0.006 0.126 2670 Dihedral : 13.998 89.358 5751 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.81 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -1.82 (0.18), residues: 1971 helix: 0.20 (0.24), residues: 441 sheet: -1.34 (0.22), residues: 495 loop : -1.77 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 57 TYR 0.014 0.002 TYR A 137 PHE 0.031 0.002 PHE B 43 TRP 0.021 0.002 TRP C 453 HIS 0.014 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00546 (15669) covalent geometry : angle 0.91814 (21198) SS BOND : bond 0.01689 ( 26) SS BOND : angle 4.09640 ( 52) hydrogen bonds : bond 0.12913 ( 629) hydrogen bonds : angle 7.14640 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6904 (tppt) cc_final: 0.6218 (ttmm) REVERT: A 196 MET cc_start: 0.8381 (ptm) cc_final: 0.8154 (ptm) REVERT: A 343 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 350 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.7038 (ttp80) REVERT: A 453 TRP cc_start: 0.6348 (p-90) cc_final: 0.5995 (p-90) REVERT: B 125 MET cc_start: 0.6892 (mmt) cc_final: 0.5902 (mmt) REVERT: B 133 GLU cc_start: 0.8467 (mp0) cc_final: 0.8204 (tm-30) REVERT: B 201 MET cc_start: 0.7558 (mtp) cc_final: 0.6892 (mtp) REVERT: B 237 LEU cc_start: 0.9254 (mm) cc_final: 0.8967 (tp) REVERT: B 260 MET cc_start: 0.8295 (mmp) cc_final: 0.8023 (mmm) REVERT: C 42 ASP cc_start: 0.7054 (t0) cc_final: 0.6672 (t0) REVERT: C 375 ASP cc_start: 0.8700 (m-30) cc_final: 0.8157 (t0) REVERT: C 394 LYS cc_start: 0.8893 (mmtm) cc_final: 0.7858 (tmtt) REVERT: D 2 HIS cc_start: 0.5573 (m-70) cc_final: 0.5330 (m-70) REVERT: D 13 ILE cc_start: 0.9011 (mp) cc_final: 0.8530 (pt) REVERT: D 37 MET cc_start: 0.6494 (tpt) cc_final: 0.6148 (tpt) REVERT: D 41 LEU cc_start: 0.9147 (tp) cc_final: 0.8919 (tp) REVERT: D 52 LYS cc_start: 0.7253 (mmtm) cc_final: 0.5474 (ttmm) REVERT: D 110 TRP cc_start: 0.6239 (m-90) cc_final: 0.5895 (m-90) REVERT: D 136 MET cc_start: 0.3700 (tmm) cc_final: 0.2389 (tpt) REVERT: E 37 MET cc_start: 0.7754 (mmp) cc_final: 0.6439 (mtm) REVERT: E 56 LEU cc_start: 0.8205 (mm) cc_final: 0.7419 (tt) REVERT: E 122 ARG cc_start: 0.4570 (ttt180) cc_final: 0.2881 (mmt180) REVERT: E 129 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7788 (ttm-80) REVERT: F 17 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 47 ASP cc_start: 0.8065 (m-30) cc_final: 0.7843 (m-30) REVERT: F 63 ASP cc_start: 0.6277 (t0) cc_final: 0.5970 (t0) REVERT: F 136 MET cc_start: 0.7206 (ptm) cc_final: 0.6733 (ppp) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2678 time to fit residues: 174.0867 Evaluate side-chains 376 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 355 ASN C 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.180141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.147792 restraints weight = 106281.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.154167 restraints weight = 46106.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.158328 restraints weight = 25773.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.160835 restraints weight = 16938.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.162572 restraints weight = 12735.297| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 15695 Z= 0.150 Angle : 0.695 30.460 21250 Z= 0.364 Chirality : 0.044 0.325 2418 Planarity : 0.005 0.059 2670 Dihedral : 5.800 39.002 2091 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.65 % Favored : 93.15 % Rotamer: Outliers : 0.12 % Allowed : 2.01 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.86 (0.18), residues: 1971 helix: 0.42 (0.23), residues: 442 sheet: -1.50 (0.22), residues: 491 loop : -1.85 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.009 0.001 TYR F 51 PHE 0.027 0.001 PHE F 155 TRP 0.012 0.001 TRP C 453 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00350 (15669) covalent geometry : angle 0.67085 (21198) SS BOND : bond 0.00890 ( 26) SS BOND : angle 3.74007 ( 52) hydrogen bonds : bond 0.05082 ( 629) hydrogen bonds : angle 6.33758 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6299 (tppt) cc_final: 0.5675 (ttmm) REVERT: A 183 MET cc_start: 0.5832 (mmp) cc_final: 0.5495 (mmp) REVERT: A 196 MET cc_start: 0.8337 (ptm) cc_final: 0.8127 (ptm) REVERT: A 343 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 453 TRP cc_start: 0.6257 (p-90) cc_final: 0.6010 (p-90) REVERT: B 133 GLU cc_start: 0.8563 (mp0) cc_final: 0.8317 (tm-30) REVERT: B 237 LEU cc_start: 0.9208 (mm) cc_final: 0.8724 (tp) REVERT: B 334 LYS cc_start: 0.7492 (tttm) cc_final: 0.7201 (tttm) REVERT: C 42 ASP cc_start: 0.7191 (t0) cc_final: 0.6737 (t0) REVERT: C 375 ASP cc_start: 0.8552 (m-30) cc_final: 0.8108 (t0) REVERT: C 386 GLN cc_start: 0.8398 (tp40) cc_final: 0.8146 (tp40) REVERT: C 394 LYS cc_start: 0.8922 (mmtm) cc_final: 0.7748 (tmtt) REVERT: D 49 ILE cc_start: 0.7545 (mm) cc_final: 0.7280 (tp) REVERT: D 136 MET cc_start: 0.3602 (tmm) cc_final: 0.3316 (tmm) REVERT: E 37 MET cc_start: 0.7831 (mmp) cc_final: 0.6613 (mtm) REVERT: E 122 ARG cc_start: 0.4466 (ttt180) cc_final: 0.2915 (mmt180) REVERT: E 129 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7676 (ttm-80) REVERT: F 17 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7105 (tm-30) REVERT: F 47 ASP cc_start: 0.8119 (m-30) cc_final: 0.7853 (m-30) REVERT: F 63 ASP cc_start: 0.6342 (t0) cc_final: 0.6019 (t0) outliers start: 2 outliers final: 1 residues processed: 429 average time/residue: 0.2862 time to fit residues: 185.0371 Evaluate side-chains 378 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 87 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS C 94 HIS D 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.180300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148271 restraints weight = 107348.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154542 restraints weight = 47269.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.158604 restraints weight = 26583.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.161187 restraints weight = 17649.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.162816 restraints weight = 13255.614| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 15695 Z= 0.146 Angle : 0.674 30.553 21250 Z= 0.351 Chirality : 0.044 0.321 2418 Planarity : 0.005 0.125 2670 Dihedral : 5.588 34.837 2091 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.10 % Favored : 92.69 % Rotamer: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.76 (0.18), residues: 1971 helix: 0.65 (0.24), residues: 443 sheet: -1.47 (0.22), residues: 502 loop : -1.85 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 87 TYR 0.009 0.001 TYR C 299 PHE 0.024 0.001 PHE F 155 TRP 0.011 0.001 TRP C 220 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00348 (15669) covalent geometry : angle 0.65092 (21198) SS BOND : bond 0.01013 ( 26) SS BOND : angle 3.58653 ( 52) hydrogen bonds : bond 0.04597 ( 629) hydrogen bonds : angle 6.02005 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6301 (tppt) cc_final: 0.5679 (ttmm) REVERT: A 180 THR cc_start: 0.7217 (p) cc_final: 0.6934 (p) REVERT: A 183 MET cc_start: 0.5849 (mmp) cc_final: 0.5396 (mmp) REVERT: A 312 ILE cc_start: 0.7955 (tt) cc_final: 0.7734 (tt) REVERT: A 343 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 392 PHE cc_start: 0.8198 (t80) cc_final: 0.7500 (p90) REVERT: A 453 TRP cc_start: 0.6207 (p-90) cc_final: 0.5951 (p-90) REVERT: B 133 GLU cc_start: 0.8582 (mp0) cc_final: 0.8330 (tm-30) REVERT: B 237 LEU cc_start: 0.9018 (mm) cc_final: 0.8592 (tp) REVERT: B 260 MET cc_start: 0.8246 (mmp) cc_final: 0.7971 (mmm) REVERT: B 334 LYS cc_start: 0.7644 (tttm) cc_final: 0.7351 (tttm) REVERT: B 380 ILE cc_start: 0.7935 (mm) cc_final: 0.7724 (mm) REVERT: C 42 ASP cc_start: 0.7223 (t0) cc_final: 0.6646 (t0) REVERT: C 375 ASP cc_start: 0.8572 (m-30) cc_final: 0.7649 (t0) REVERT: C 392 PHE cc_start: 0.8045 (t80) cc_final: 0.7185 (t80) REVERT: D 37 MET cc_start: 0.7025 (tpt) cc_final: 0.6366 (tpt) REVERT: D 49 ILE cc_start: 0.7523 (mm) cc_final: 0.7268 (tp) REVERT: D 52 LYS cc_start: 0.6555 (mmmm) cc_final: 0.5143 (tttt) REVERT: D 136 MET cc_start: 0.3634 (tmm) cc_final: 0.3390 (tmm) REVERT: E 37 MET cc_start: 0.7812 (mmp) cc_final: 0.6269 (mtp) REVERT: E 122 ARG cc_start: 0.4441 (ttt180) cc_final: 0.2870 (mmt180) REVERT: E 129 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7652 (ttm-80) REVERT: F 47 ASP cc_start: 0.8186 (m-30) cc_final: 0.7898 (m-30) REVERT: F 63 ASP cc_start: 0.6402 (t0) cc_final: 0.6074 (t0) outliers start: 1 outliers final: 1 residues processed: 423 average time/residue: 0.2738 time to fit residues: 176.8806 Evaluate side-chains 383 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 437 HIS C 94 HIS ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.166014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130350 restraints weight = 109448.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136546 restraints weight = 50503.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140604 restraints weight = 29523.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.143203 restraints weight = 20220.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144867 restraints weight = 15597.306| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 15695 Z= 0.211 Angle : 0.700 29.209 21250 Z= 0.368 Chirality : 0.043 0.346 2418 Planarity : 0.006 0.130 2670 Dihedral : 5.620 32.038 2091 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.07 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.78 (0.18), residues: 1971 helix: 0.79 (0.24), residues: 444 sheet: -1.47 (0.22), residues: 504 loop : -1.96 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 6 TYR 0.013 0.002 TYR A 444 PHE 0.024 0.002 PHE F 155 TRP 0.013 0.001 TRP D 74 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00470 (15669) covalent geometry : angle 0.68041 (21198) SS BOND : bond 0.00922 ( 26) SS BOND : angle 3.43406 ( 52) hydrogen bonds : bond 0.04628 ( 629) hydrogen bonds : angle 5.86952 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6509 (tppt) cc_final: 0.5883 (ttmm) REVERT: A 103 ASN cc_start: 0.7184 (m110) cc_final: 0.6905 (m110) REVERT: A 180 THR cc_start: 0.7481 (p) cc_final: 0.7223 (p) REVERT: A 183 MET cc_start: 0.6096 (mmp) cc_final: 0.5511 (mmp) REVERT: A 312 ILE cc_start: 0.8006 (tt) cc_final: 0.7598 (tt) REVERT: A 343 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8421 (tm-30) REVERT: A 453 TRP cc_start: 0.5971 (p-90) cc_final: 0.5621 (p-90) REVERT: B 30 CYS cc_start: 0.3546 (t) cc_final: 0.3272 (t) REVERT: B 38 LYS cc_start: 0.7646 (tptt) cc_final: 0.7318 (tppt) REVERT: B 133 GLU cc_start: 0.8658 (mp0) cc_final: 0.8415 (tm-30) REVERT: B 211 GLN cc_start: 0.9167 (pm20) cc_final: 0.8966 (pm20) REVERT: B 237 LEU cc_start: 0.9191 (mm) cc_final: 0.8830 (tp) REVERT: C 92 CYS cc_start: 0.3078 (p) cc_final: 0.2849 (p) REVERT: C 287 LEU cc_start: 0.7324 (mt) cc_final: 0.6797 (mt) REVERT: C 375 ASP cc_start: 0.8538 (m-30) cc_final: 0.7712 (t0) REVERT: C 392 PHE cc_start: 0.7987 (t80) cc_final: 0.7179 (t80) REVERT: D 37 MET cc_start: 0.7323 (tpt) cc_final: 0.6936 (tpt) REVERT: D 52 LYS cc_start: 0.6965 (mmmm) cc_final: 0.5987 (tttt) REVERT: D 64 ILE cc_start: 0.8299 (mm) cc_final: 0.8091 (mm) REVERT: D 136 MET cc_start: 0.3639 (tmm) cc_final: 0.3387 (tmm) REVERT: E 37 MET cc_start: 0.7898 (mmp) cc_final: 0.6640 (mtm) REVERT: E 122 ARG cc_start: 0.4420 (ttt180) cc_final: 0.3066 (mmt180) REVERT: E 129 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7665 (ttm-80) REVERT: F 37 MET cc_start: 0.7007 (ttp) cc_final: 0.6784 (ttm) REVERT: F 47 ASP cc_start: 0.8180 (m-30) cc_final: 0.7891 (m-30) REVERT: F 63 ASP cc_start: 0.6585 (t0) cc_final: 0.6281 (t0) REVERT: F 133 PHE cc_start: 0.6028 (m-80) cc_final: 0.5806 (m-80) REVERT: F 136 MET cc_start: 0.7221 (ptm) cc_final: 0.6768 (ppp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2685 time to fit residues: 172.6408 Evaluate side-chains 368 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS C 94 HIS C 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134702 restraints weight = 107568.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140870 restraints weight = 49701.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144905 restraints weight = 28907.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.147479 restraints weight = 19628.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149103 restraints weight = 14982.530| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 : 0.004 0.141 15695 Z= 0.148 Angle : 0.666 29.225 21250 Z= 0.347 Chirality : 0.044 0.312 2418 Planarity : 0.005 0.136 2670 Dihedral : 5.472 31.759 2091 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.00 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.67 (0.18), residues: 1971 helix: 0.89 (0.24), residues: 445 sheet: -1.41 (0.22), residues: 509 loop : -1.88 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 57 TYR 0.011 0.001 TYR A 444 PHE 0.024 0.001 PHE F 155 TRP 0.014 0.001 TRP B 231 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00353 (15669) covalent geometry : angle 0.64307 (21198) SS BOND : bond 0.00889 ( 26) SS BOND : angle 3.54801 ( 52) hydrogen bonds : bond 0.04326 ( 629) hydrogen bonds : angle 5.74599 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7211 (m110) cc_final: 0.6899 (m110) REVERT: A 180 THR cc_start: 0.7514 (p) cc_final: 0.7225 (p) REVERT: A 183 MET cc_start: 0.6101 (mmp) cc_final: 0.5445 (mmp) REVERT: A 312 ILE cc_start: 0.7972 (tt) cc_final: 0.7537 (tt) REVERT: A 343 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 34 MET cc_start: 0.8574 (mtt) cc_final: 0.8123 (mtt) REVERT: B 38 LYS cc_start: 0.7605 (tptt) cc_final: 0.7261 (tppt) REVERT: B 133 GLU cc_start: 0.8658 (mp0) cc_final: 0.8414 (tm-30) REVERT: B 237 LEU cc_start: 0.9035 (mm) cc_final: 0.8673 (tp) REVERT: B 334 LYS cc_start: 0.7682 (tttm) cc_final: 0.7416 (tttm) REVERT: C 42 ASP cc_start: 0.7324 (t0) cc_final: 0.6734 (t0) REVERT: C 137 TYR cc_start: 0.7979 (m-80) cc_final: 0.7635 (m-80) REVERT: C 375 ASP cc_start: 0.8498 (m-30) cc_final: 0.7671 (t0) REVERT: C 392 PHE cc_start: 0.7944 (t80) cc_final: 0.7137 (t80) REVERT: D 37 MET cc_start: 0.7274 (tpt) cc_final: 0.6934 (tpt) REVERT: D 49 ILE cc_start: 0.7773 (mm) cc_final: 0.7469 (tp) REVERT: D 52 LYS cc_start: 0.6800 (mmmm) cc_final: 0.5735 (tttt) REVERT: D 64 ILE cc_start: 0.8449 (mm) cc_final: 0.8237 (mm) REVERT: D 136 MET cc_start: 0.3612 (tmm) cc_final: 0.3373 (tmm) REVERT: E 37 MET cc_start: 0.7815 (mmp) cc_final: 0.6510 (mtp) REVERT: E 56 LEU cc_start: 0.8195 (mm) cc_final: 0.7417 (tt) REVERT: E 122 ARG cc_start: 0.4401 (ttt180) cc_final: 0.3048 (mmt180) REVERT: E 129 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7639 (ttm-80) REVERT: F 37 MET cc_start: 0.7018 (ttp) cc_final: 0.6748 (ttm) REVERT: F 47 ASP cc_start: 0.8102 (m-30) cc_final: 0.7850 (m-30) REVERT: F 63 ASP cc_start: 0.6630 (t0) cc_final: 0.6291 (t0) REVERT: F 133 PHE cc_start: 0.6053 (m-80) cc_final: 0.5831 (m-80) REVERT: F 136 MET cc_start: 0.7239 (ptm) cc_final: 0.6762 (ppp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2721 time to fit residues: 174.4677 Evaluate side-chains 371 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 180 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132387 restraints weight = 111130.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138622 restraints weight = 50678.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142693 restraints weight = 29333.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145346 restraints weight = 19863.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147062 restraints weight = 15122.026| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 15695 Z= 0.167 Angle : 0.672 28.639 21250 Z= 0.350 Chirality : 0.044 0.361 2418 Planarity : 0.005 0.106 2670 Dihedral : 5.412 30.761 2091 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.32 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.70 (0.18), residues: 1971 helix: 0.83 (0.24), residues: 448 sheet: -1.36 (0.22), residues: 505 loop : -1.94 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 407 TYR 0.012 0.001 TYR B 444 PHE 0.024 0.001 PHE F 155 TRP 0.012 0.001 TRP D 74 HIS 0.005 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00385 (15669) covalent geometry : angle 0.64979 (21198) SS BOND : bond 0.00907 ( 26) SS BOND : angle 3.52167 ( 52) hydrogen bonds : bond 0.04436 ( 629) hydrogen bonds : angle 5.55806 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7210 (m110) cc_final: 0.7005 (m110) REVERT: A 158 HIS cc_start: 0.5609 (m-70) cc_final: 0.5375 (m-70) REVERT: A 180 THR cc_start: 0.7630 (p) cc_final: 0.7315 (p) REVERT: A 183 MET cc_start: 0.6251 (mmp) cc_final: 0.5503 (mmp) REVERT: A 282 HIS cc_start: 0.8472 (m90) cc_final: 0.7753 (m90) REVERT: A 312 ILE cc_start: 0.7960 (tt) cc_final: 0.7633 (tt) REVERT: A 343 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 368 GLU cc_start: 0.7911 (tp30) cc_final: 0.7682 (mm-30) REVERT: A 401 MET cc_start: 0.8267 (mmm) cc_final: 0.8041 (mmm) REVERT: B 38 LYS cc_start: 0.7684 (tptt) cc_final: 0.7374 (tppt) REVERT: B 125 MET cc_start: 0.7355 (mmm) cc_final: 0.6094 (mmt) REVERT: B 133 GLU cc_start: 0.8686 (mp0) cc_final: 0.8423 (tm-30) REVERT: B 201 MET cc_start: 0.7708 (mtm) cc_final: 0.6794 (mtm) REVERT: B 237 LEU cc_start: 0.9121 (mm) cc_final: 0.8765 (tp) REVERT: B 260 MET cc_start: 0.8498 (mmp) cc_final: 0.8074 (mmm) REVERT: C 40 THR cc_start: 0.8908 (p) cc_final: 0.8425 (p) REVERT: C 42 ASP cc_start: 0.7315 (t0) cc_final: 0.6710 (t0) REVERT: C 137 TYR cc_start: 0.8014 (m-80) cc_final: 0.7628 (m-80) REVERT: C 375 ASP cc_start: 0.8593 (m-30) cc_final: 0.7722 (t0) REVERT: C 392 PHE cc_start: 0.7894 (t80) cc_final: 0.7153 (t80) REVERT: D 37 MET cc_start: 0.7312 (tpt) cc_final: 0.7092 (tpt) REVERT: D 49 ILE cc_start: 0.7644 (mm) cc_final: 0.7410 (tp) REVERT: D 52 LYS cc_start: 0.6810 (mmmm) cc_final: 0.5675 (tttt) REVERT: D 64 ILE cc_start: 0.8328 (mm) cc_final: 0.8107 (mm) REVERT: D 136 MET cc_start: 0.3645 (tmm) cc_final: 0.3400 (tmm) REVERT: E 37 MET cc_start: 0.7889 (mmp) cc_final: 0.6606 (mtp) REVERT: E 122 ARG cc_start: 0.4226 (ttt180) cc_final: 0.2877 (mmt180) REVERT: E 129 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7678 (ttm-80) REVERT: F 37 MET cc_start: 0.7098 (ttp) cc_final: 0.6745 (ttm) REVERT: F 47 ASP cc_start: 0.8150 (m-30) cc_final: 0.7901 (m-30) REVERT: F 63 ASP cc_start: 0.6696 (t0) cc_final: 0.6385 (t0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.2775 time to fit residues: 177.1530 Evaluate side-chains 368 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 0.0970 chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN F 32 ASN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.170815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.136365 restraints weight = 107859.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.142424 restraints weight = 47994.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.146350 restraints weight = 27424.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.148870 restraints weight = 18546.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.150471 restraints weight = 14193.797| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 15695 Z= 0.260 Angle : 0.747 29.490 21250 Z= 0.394 Chirality : 0.044 0.340 2418 Planarity : 0.006 0.182 2670 Dihedral : 5.697 30.092 2091 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.28 % Favored : 90.51 % Rotamer: Outliers : 0.06 % Allowed : 1.47 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.91 (0.18), residues: 1971 helix: 0.79 (0.24), residues: 448 sheet: -1.36 (0.22), residues: 517 loop : -2.23 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 288 TYR 0.014 0.002 TYR F 51 PHE 0.024 0.002 PHE F 155 TRP 0.032 0.002 TRP C 20 HIS 0.017 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00575 (15669) covalent geometry : angle 0.72563 (21198) SS BOND : bond 0.00897 ( 26) SS BOND : angle 3.67694 ( 52) hydrogen bonds : bond 0.04786 ( 629) hydrogen bonds : angle 5.67356 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7442 (m110) cc_final: 0.7119 (m110) REVERT: A 183 MET cc_start: 0.6692 (mmp) cc_final: 0.5953 (mmp) REVERT: A 215 ASP cc_start: 0.8627 (m-30) cc_final: 0.8387 (m-30) REVERT: A 312 ILE cc_start: 0.8036 (tt) cc_final: 0.7748 (tt) REVERT: A 343 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 401 MET cc_start: 0.8221 (mmm) cc_final: 0.7977 (mmm) REVERT: B 6 ILE cc_start: 0.8832 (mm) cc_final: 0.8422 (mm) REVERT: B 34 MET cc_start: 0.8582 (mtt) cc_final: 0.8276 (mtt) REVERT: B 52 GLN cc_start: 0.7994 (mm110) cc_final: 0.7792 (mm110) REVERT: B 133 GLU cc_start: 0.8738 (mp0) cc_final: 0.8468 (tm-30) REVERT: B 237 LEU cc_start: 0.9119 (mm) cc_final: 0.8777 (tp) REVERT: B 334 LYS cc_start: 0.7707 (tttm) cc_final: 0.7479 (tttm) REVERT: C 42 ASP cc_start: 0.7443 (t0) cc_final: 0.6917 (t0) REVERT: C 137 TYR cc_start: 0.8150 (m-80) cc_final: 0.7669 (m-80) REVERT: C 283 LEU cc_start: 0.8694 (tp) cc_final: 0.8449 (tp) REVERT: C 375 ASP cc_start: 0.8699 (m-30) cc_final: 0.8307 (t0) REVERT: C 448 PHE cc_start: 0.7438 (m-10) cc_final: 0.7015 (m-10) REVERT: D 52 LYS cc_start: 0.7142 (mmmm) cc_final: 0.6077 (tttt) REVERT: D 136 MET cc_start: 0.3489 (tmm) cc_final: 0.3237 (tmm) REVERT: E 7 ASN cc_start: 0.8932 (t0) cc_final: 0.8699 (t0) REVERT: E 37 MET cc_start: 0.8143 (mmp) cc_final: 0.6886 (mtm) REVERT: E 56 LEU cc_start: 0.8403 (mm) cc_final: 0.7569 (tt) REVERT: E 122 ARG cc_start: 0.4250 (ttt180) cc_final: 0.2906 (mmt180) REVERT: E 129 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7672 (ttm-80) REVERT: F 47 ASP cc_start: 0.8360 (m-30) cc_final: 0.8095 (m-30) REVERT: F 63 ASP cc_start: 0.6960 (t0) cc_final: 0.6634 (t0) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.2769 time to fit residues: 173.6951 Evaluate side-chains 357 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.165056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130224 restraints weight = 107285.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136298 restraints weight = 50072.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140231 restraints weight = 29336.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142745 restraints weight = 20147.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.144323 restraints weight = 15562.107| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 15695 Z= 0.169 Angle : 0.697 30.869 21250 Z= 0.363 Chirality : 0.045 0.346 2418 Planarity : 0.005 0.120 2670 Dihedral : 5.550 31.047 2091 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.56 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.78 (0.18), residues: 1971 helix: 0.88 (0.24), residues: 449 sheet: -1.28 (0.22), residues: 506 loop : -2.14 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 407 TYR 0.014 0.002 TYR C 299 PHE 0.024 0.001 PHE F 155 TRP 0.037 0.001 TRP A 391 HIS 0.008 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00405 (15669) covalent geometry : angle 0.67046 (21198) SS BOND : bond 0.00984 ( 26) SS BOND : angle 3.89625 ( 52) hydrogen bonds : bond 0.04366 ( 629) hydrogen bonds : angle 5.51410 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.5662 (m-70) cc_final: 0.5445 (m-70) REVERT: A 183 MET cc_start: 0.6496 (mmp) cc_final: 0.5831 (mmp) REVERT: A 201 MET cc_start: 0.8115 (mtt) cc_final: 0.7850 (mtt) REVERT: A 272 MET cc_start: 0.8714 (ptm) cc_final: 0.8142 (ppp) REVERT: A 343 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 392 PHE cc_start: 0.8381 (t80) cc_final: 0.7950 (t80) REVERT: A 401 MET cc_start: 0.8164 (mmm) cc_final: 0.7892 (mmm) REVERT: B 34 MET cc_start: 0.8597 (mtt) cc_final: 0.8231 (mtt) REVERT: B 38 LYS cc_start: 0.8021 (tptt) cc_final: 0.7521 (tppt) REVERT: B 133 GLU cc_start: 0.8645 (mp0) cc_final: 0.8409 (tm-30) REVERT: B 237 LEU cc_start: 0.9122 (mm) cc_final: 0.8814 (tp) REVERT: B 303 THR cc_start: 0.7980 (p) cc_final: 0.7682 (t) REVERT: B 334 LYS cc_start: 0.7566 (tttm) cc_final: 0.7337 (tttm) REVERT: C 42 ASP cc_start: 0.6922 (t0) cc_final: 0.6505 (t0) REVERT: C 137 TYR cc_start: 0.8075 (m-80) cc_final: 0.7696 (m-80) REVERT: C 375 ASP cc_start: 0.8582 (m-30) cc_final: 0.7831 (t0) REVERT: C 392 PHE cc_start: 0.7976 (t80) cc_final: 0.7209 (t80) REVERT: C 448 PHE cc_start: 0.7353 (m-10) cc_final: 0.6932 (m-10) REVERT: D 41 LEU cc_start: 0.9349 (tp) cc_final: 0.9148 (tp) REVERT: D 52 LYS cc_start: 0.6996 (mmmm) cc_final: 0.5746 (tttp) REVERT: D 136 MET cc_start: 0.3544 (tmm) cc_final: 0.3290 (tmm) REVERT: E 7 ASN cc_start: 0.8904 (t0) cc_final: 0.8690 (t0) REVERT: E 37 MET cc_start: 0.7999 (mmp) cc_final: 0.6794 (mtm) REVERT: E 56 LEU cc_start: 0.8496 (mm) cc_final: 0.7674 (tt) REVERT: E 129 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7671 (ttm-80) REVERT: F 63 ASP cc_start: 0.7025 (t0) cc_final: 0.6719 (t0) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2771 time to fit residues: 177.0020 Evaluate side-chains 357 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128395 restraints weight = 109047.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134226 restraints weight = 52329.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138074 restraints weight = 31235.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140524 restraints weight = 21760.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.142080 restraints weight = 16983.762| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 15695 Z= 0.196 Angle : 0.704 31.028 21250 Z= 0.368 Chirality : 0.044 0.359 2418 Planarity : 0.005 0.117 2670 Dihedral : 5.544 30.197 2091 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.37 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.77 (0.18), residues: 1971 helix: 0.94 (0.24), residues: 449 sheet: -1.26 (0.22), residues: 517 loop : -2.16 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 407 TYR 0.010 0.002 TYR F 51 PHE 0.024 0.001 PHE F 155 TRP 0.013 0.001 TRP D 74 HIS 0.012 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00454 (15669) covalent geometry : angle 0.67786 (21198) SS BOND : bond 0.01147 ( 26) SS BOND : angle 3.89705 ( 52) hydrogen bonds : bond 0.04475 ( 629) hydrogen bonds : angle 5.50317 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6913 (tppt) cc_final: 0.6279 (ttmm) REVERT: A 158 HIS cc_start: 0.5719 (m-70) cc_final: 0.5507 (m-70) REVERT: A 201 MET cc_start: 0.8179 (mtt) cc_final: 0.7880 (mtt) REVERT: A 272 MET cc_start: 0.8748 (ptm) cc_final: 0.8138 (ppp) REVERT: A 282 HIS cc_start: 0.8465 (m90) cc_final: 0.7863 (m90) REVERT: A 343 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 386 GLN cc_start: 0.6692 (tp40) cc_final: 0.6478 (pm20) REVERT: A 401 MET cc_start: 0.8217 (mmm) cc_final: 0.7966 (mmm) REVERT: B 34 MET cc_start: 0.8593 (mtt) cc_final: 0.8203 (mtt) REVERT: B 38 LYS cc_start: 0.8088 (tptt) cc_final: 0.7566 (tppt) REVERT: B 133 GLU cc_start: 0.8613 (mp0) cc_final: 0.8358 (tm-30) REVERT: B 237 LEU cc_start: 0.9226 (mm) cc_final: 0.8916 (tp) REVERT: B 303 THR cc_start: 0.7931 (p) cc_final: 0.7683 (t) REVERT: B 334 LYS cc_start: 0.7611 (tttm) cc_final: 0.7389 (tttm) REVERT: C 42 ASP cc_start: 0.7098 (t0) cc_final: 0.6657 (t0) REVERT: C 137 TYR cc_start: 0.8133 (m-80) cc_final: 0.7723 (m-80) REVERT: C 283 LEU cc_start: 0.8674 (tp) cc_final: 0.8437 (tp) REVERT: C 375 ASP cc_start: 0.8505 (m-30) cc_final: 0.7761 (t0) REVERT: C 392 PHE cc_start: 0.8023 (t80) cc_final: 0.7406 (t80) REVERT: D 41 LEU cc_start: 0.9370 (tp) cc_final: 0.9168 (tp) REVERT: D 52 LYS cc_start: 0.6962 (mmmm) cc_final: 0.5681 (tttp) REVERT: D 136 MET cc_start: 0.3391 (tmm) cc_final: 0.3130 (tmm) REVERT: E 7 ASN cc_start: 0.8917 (t0) cc_final: 0.8696 (t0) REVERT: E 37 MET cc_start: 0.8010 (mmp) cc_final: 0.6795 (mtm) REVERT: E 56 LEU cc_start: 0.8602 (mm) cc_final: 0.7808 (tt) REVERT: E 129 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7655 (ttm-80) REVERT: F 63 ASP cc_start: 0.7039 (t0) cc_final: 0.6727 (t0) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2756 time to fit residues: 170.9340 Evaluate side-chains 357 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 101 optimal weight: 0.0070 chunk 177 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132044 restraints weight = 105265.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138060 restraints weight = 48704.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142012 restraints weight = 28465.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144575 restraints weight = 19425.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.146183 restraints weight = 14884.460| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 15695 Z= 0.145 Angle : 0.689 32.534 21250 Z= 0.355 Chirality : 0.045 0.366 2418 Planarity : 0.005 0.110 2670 Dihedral : 5.392 29.723 2091 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.70 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % 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 aren not related in a simple way. whole: -1.59 (0.19), residues: 1971 helix: 1.02 (0.24), residues: 450 sheet: -1.16 (0.23), residues: 517 loop : -2.02 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 407 TYR 0.009 0.001 TYR C 444 PHE 0.025 0.001 PHE F 155 TRP 0.014 0.001 TRP C 20 HIS 0.009 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00361 (15669) covalent geometry : angle 0.66324 (21198) SS BOND : bond 0.00873 ( 26) SS BOND : angle 3.79423 ( 52) hydrogen bonds : bond 0.04186 ( 629) hydrogen bonds : angle 5.37638 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6767 (tppt) cc_final: 0.6136 (ttmm) REVERT: A 158 HIS cc_start: 0.5521 (m-70) cc_final: 0.5151 (m-70) REVERT: A 201 MET cc_start: 0.8121 (mtt) cc_final: 0.7868 (mtt) REVERT: A 260 MET cc_start: 0.8729 (mmt) cc_final: 0.8472 (mmt) REVERT: A 272 MET cc_start: 0.8708 (ptm) cc_final: 0.8142 (ppp) REVERT: A 282 HIS cc_start: 0.8449 (m90) cc_final: 0.7861 (m90) REVERT: A 343 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 392 PHE cc_start: 0.8165 (t80) cc_final: 0.7842 (t80) REVERT: A 401 MET cc_start: 0.8225 (mmm) cc_final: 0.7955 (mmm) REVERT: B 38 LYS cc_start: 0.8109 (tptt) cc_final: 0.7651 (tppt) REVERT: B 133 GLU cc_start: 0.8586 (mp0) cc_final: 0.8302 (tm-30) REVERT: B 237 LEU cc_start: 0.8877 (mm) cc_final: 0.8542 (tp) REVERT: B 334 LYS cc_start: 0.7567 (tttm) cc_final: 0.7355 (tttm) REVERT: B 401 MET cc_start: 0.8065 (tpp) cc_final: 0.7791 (tpp) REVERT: C 42 ASP cc_start: 0.6800 (t0) cc_final: 0.6497 (t0) REVERT: C 283 LEU cc_start: 0.8647 (tp) cc_final: 0.8366 (tp) REVERT: C 375 ASP cc_start: 0.8578 (m-30) cc_final: 0.7870 (t0) REVERT: C 392 PHE cc_start: 0.7969 (t80) cc_final: 0.7286 (t80) REVERT: C 448 PHE cc_start: 0.7370 (m-10) cc_final: 0.6941 (m-10) REVERT: D 41 LEU cc_start: 0.9384 (tp) cc_final: 0.9169 (tp) REVERT: D 52 LYS cc_start: 0.6687 (mmmm) cc_final: 0.5417 (tttp) REVERT: D 136 MET cc_start: 0.3496 (tmm) cc_final: 0.3218 (tmm) REVERT: E 7 ASN cc_start: 0.8902 (t0) cc_final: 0.8676 (t0) REVERT: E 37 MET cc_start: 0.7968 (mmp) cc_final: 0.6652 (mtp) REVERT: E 56 LEU cc_start: 0.8508 (mm) cc_final: 0.7670 (tt) REVERT: E 129 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7626 (ttm-80) REVERT: F 25 PHE cc_start: 0.4847 (p90) cc_final: 0.4365 (p90) REVERT: F 63 ASP cc_start: 0.7024 (t0) cc_final: 0.6676 (t0) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.2740 time to fit residues: 173.2156 Evaluate side-chains 363 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 160 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.171798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.137399 restraints weight = 107674.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.143496 restraints weight = 48141.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.147446 restraints weight = 27527.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.149983 restraints weight = 18572.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.151596 restraints weight = 14179.083| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 15695 Z= 0.209 Angle : 0.712 30.120 21250 Z= 0.372 Chirality : 0.044 0.348 2418 Planarity : 0.006 0.152 2670 Dihedral : 5.458 29.687 2091 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.32 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % 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 aren not related in a simple way. whole: -1.73 (0.19), residues: 1971 helix: 0.95 (0.24), residues: 445 sheet: -1.23 (0.23), residues: 518 loop : -2.13 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 151 TYR 0.043 0.002 TYR D 142 PHE 0.033 0.002 PHE C 306 TRP 0.013 0.001 TRP E 74 HIS 0.008 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00480 (15669) covalent geometry : angle 0.68699 (21198) SS BOND : bond 0.01051 ( 26) SS BOND : angle 3.80517 ( 52) hydrogen bonds : bond 0.04422 ( 629) hydrogen bonds : angle 5.44438 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6527.57 seconds wall clock time: 112 minutes 9.93 seconds (6729.93 seconds total)