Starting phenix.real_space_refine on Wed May 28 14:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dof_47082/05_2025/9dof_47082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dof_47082/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dof_47082/05_2025/9dof_47082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dof_47082/05_2025/9dof_47082.map" model { file = "/net/cci-nas-00/data/ceres_data/9dof_47082/05_2025/9dof_47082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dof_47082/05_2025/9dof_47082.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.89, per 1000 atoms: 0.45 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: 7.81 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.87 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: 11.83 Time building geometry restraints manager: 9.41 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: 1.140 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: 0.530 Extract box with map and model: 1.180 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 62.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (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 TRP 0.021 0.002 TRP C 453 HIS 0.014 0.001 HIS C 94 PHE 0.031 0.002 PHE B 43 TYR 0.014 0.002 TYR A 137 ARG 0.022 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.12913 ( 629) hydrogen bonds : angle 7.14640 ( 1704) SS BOND : bond 0.01689 ( 26) SS BOND : angle 4.09640 ( 52) covalent geometry : bond 0.00546 (15669) covalent geometry : angle 0.91814 (21198) *********************** 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 : 2.616 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: 0.5474 time to fit residues: 354.0808 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 : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.186065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.151833 restraints weight = 109340.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158227 restraints weight = 48637.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.162332 restraints weight = 27591.012| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 15695 Z= 0.174 Angle : 0.706 30.049 21250 Z= 0.371 Chirality : 0.044 0.320 2418 Planarity : 0.005 0.059 2670 Dihedral : 5.835 38.555 2091 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.05 % Favored : 92.74 % Rotamer: Outliers : 0.12 % Allowed : 2.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.18), residues: 1971 helix: 0.44 (0.24), residues: 443 sheet: -1.53 (0.22), residues: 498 loop : -1.88 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 453 HIS 0.006 0.001 HIS C 94 PHE 0.028 0.001 PHE F 155 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 629) hydrogen bonds : angle 6.32685 ( 1704) SS BOND : bond 0.00883 ( 26) SS BOND : angle 3.76702 ( 52) covalent geometry : bond 0.00397 (15669) covalent geometry : angle 0.68182 (21198) *********************** 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 424 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 2.444 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: A 64 LYS cc_start: 0.6390 (tppt) cc_final: 0.5747 (ttmm) REVERT: A 103 ASN cc_start: 0.7257 (m110) cc_final: 0.6934 (m110) REVERT: A 183 MET cc_start: 0.6143 (mmp) cc_final: 0.5707 (mmp) REVERT: A 196 MET cc_start: 0.8402 (ptm) cc_final: 0.8154 (ptm) REVERT: A 312 ILE cc_start: 0.8000 (tt) cc_final: 0.7744 (tt) REVERT: A 343 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 350 ARG cc_start: 0.6897 (ttp-110) cc_final: 0.6634 (ttp-110) REVERT: A 453 TRP cc_start: 0.6174 (p-90) cc_final: 0.5920 (p-90) REVERT: B 125 MET cc_start: 0.6532 (mmt) cc_final: 0.4906 (mmt) REVERT: B 133 GLU cc_start: 0.8612 (mp0) cc_final: 0.8325 (tm-30) REVERT: B 201 MET cc_start: 0.7374 (mtp) cc_final: 0.6810 (mtp) REVERT: B 237 LEU cc_start: 0.9260 (mm) cc_final: 0.8774 (tp) REVERT: B 334 LYS cc_start: 0.7554 (tttm) cc_final: 0.7252 (tttm) REVERT: C 42 ASP cc_start: 0.7353 (t0) cc_final: 0.6815 (t0) REVERT: C 118 MET cc_start: 0.5921 (tpt) cc_final: 0.5711 (tpt) REVERT: C 375 ASP cc_start: 0.8710 (m-30) cc_final: 0.8231 (t0) REVERT: C 394 LYS cc_start: 0.8955 (mmtm) cc_final: 0.7816 (tmtt) REVERT: D 49 ILE cc_start: 0.7616 (mm) cc_final: 0.7343 (tp) REVERT: D 64 ILE cc_start: 0.8432 (mm) cc_final: 0.8206 (mm) REVERT: D 136 MET cc_start: 0.3418 (tmm) cc_final: 0.3151 (tmm) REVERT: E 35 THR cc_start: 0.8280 (m) cc_final: 0.8072 (m) REVERT: E 37 MET cc_start: 0.7933 (mmp) cc_final: 0.6739 (mtm) REVERT: E 122 ARG cc_start: 0.4435 (ttt180) cc_final: 0.2879 (mmt180) REVERT: E 129 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7661 (ttm-80) REVERT: F 47 ASP cc_start: 0.8196 (m-30) cc_final: 0.7835 (m-30) REVERT: F 63 ASP cc_start: 0.6373 (t0) cc_final: 0.6038 (t0) outliers start: 2 outliers final: 1 residues processed: 423 average time/residue: 0.5811 time to fit residues: 370.6099 Evaluate side-chains 371 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 ** 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 = 0.4524 r_free = 0.4524 target = 0.184494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.150910 restraints weight = 109923.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.157217 restraints weight = 48189.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.161287 restraints weight = 27086.788| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 15695 Z= 0.181 Angle : 0.693 30.573 21250 Z= 0.363 Chirality : 0.044 0.308 2418 Planarity : 0.005 0.130 2670 Dihedral : 5.689 34.687 2091 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.71 % Favored : 92.09 % Rotamer: Outliers : 0.06 % Allowed : 2.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 1971 helix: 0.67 (0.24), residues: 443 sheet: -1.50 (0.22), residues: 502 loop : -1.92 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.007 0.001 HIS B 437 PHE 0.024 0.001 PHE F 155 TYR 0.010 0.001 TYR C 299 ARG 0.008 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 629) hydrogen bonds : angle 6.02191 ( 1704) SS BOND : bond 0.00551 ( 26) SS BOND : angle 3.56245 ( 52) covalent geometry : bond 0.00413 (15669) covalent geometry : angle 0.67088 (21198) *********************** 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 425 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 2.390 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: 0.6514 (tppt) cc_final: 0.5881 (ttmm) REVERT: A 103 ASN cc_start: 0.7334 (m110) cc_final: 0.7105 (m110) REVERT: A 180 THR cc_start: 0.7430 (p) cc_final: 0.7151 (p) REVERT: A 183 MET cc_start: 0.6130 (mmp) cc_final: 0.5569 (mmp) REVERT: A 196 MET cc_start: 0.8379 (ptm) cc_final: 0.8136 (ptm) REVERT: A 312 ILE cc_start: 0.8032 (tt) cc_final: 0.7707 (tt) REVERT: A 343 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 350 ARG cc_start: 0.7036 (ttp-110) cc_final: 0.6800 (ttp-110) REVERT: A 453 TRP cc_start: 0.6153 (p-90) cc_final: 0.5876 (p-90) REVERT: B 38 LYS cc_start: 0.7609 (tptt) cc_final: 0.7260 (tppt) REVERT: B 133 GLU cc_start: 0.8627 (mp0) cc_final: 0.8347 (tm-30) REVERT: B 237 LEU cc_start: 0.9080 (mm) cc_final: 0.8684 (tp) REVERT: B 260 MET cc_start: 0.8286 (mmp) cc_final: 0.8030 (mmm) REVERT: B 334 LYS cc_start: 0.7734 (tttm) cc_final: 0.7479 (tttm) REVERT: C 42 ASP cc_start: 0.7346 (t0) cc_final: 0.6755 (t0) REVERT: C 92 CYS cc_start: 0.2946 (p) cc_final: 0.2688 (p) REVERT: C 375 ASP cc_start: 0.8700 (m-30) cc_final: 0.8250 (t0) REVERT: C 394 LYS cc_start: 0.8776 (mptt) cc_final: 0.8350 (tmtt) REVERT: D 37 MET cc_start: 0.7267 (tpt) cc_final: 0.6853 (tpt) REVERT: D 49 ILE cc_start: 0.7731 (mm) cc_final: 0.7452 (tp) REVERT: D 52 LYS cc_start: 0.6799 (mmmm) cc_final: 0.5329 (tttt) REVERT: D 64 ILE cc_start: 0.8578 (mm) cc_final: 0.8369 (mm) REVERT: D 136 MET cc_start: 0.3528 (tmm) cc_final: 0.3293 (tmm) REVERT: E 37 MET cc_start: 0.7864 (mmp) cc_final: 0.6438 (mtp) REVERT: E 56 LEU cc_start: 0.8254 (mm) cc_final: 0.7395 (tt) REVERT: E 122 ARG cc_start: 0.4417 (ttt180) cc_final: 0.3091 (mmt180) REVERT: E 129 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7677 (ttm-80) REVERT: F 47 ASP cc_start: 0.8289 (m-30) cc_final: 0.7956 (m-30) REVERT: F 63 ASP cc_start: 0.6482 (t0) cc_final: 0.6141 (t0) REVERT: F 136 MET cc_start: 0.7192 (ptm) cc_final: 0.6748 (ppp) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.5503 time to fit residues: 350.7838 Evaluate side-chains 376 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 146 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4171 r_free = 0.4171 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128420 restraints weight = 107145.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134292 restraints weight = 50279.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138198 restraints weight = 29774.049| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 15695 Z= 0.261 Angle : 0.735 28.258 21250 Z= 0.389 Chirality : 0.044 0.326 2418 Planarity : 0.005 0.086 2670 Dihedral : 5.806 32.468 2091 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.03 % Favored : 90.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1971 helix: 0.66 (0.24), residues: 447 sheet: -1.49 (0.22), residues: 518 loop : -2.17 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 74 HIS 0.005 0.001 HIS E 130 PHE 0.023 0.002 PHE F 155 TYR 0.015 0.002 TYR A 444 ARG 0.011 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 629) hydrogen bonds : angle 5.98787 ( 1704) SS BOND : bond 0.00959 ( 26) SS BOND : angle 3.68444 ( 52) covalent geometry : bond 0.00576 (15669) covalent geometry : angle 0.71312 (21198) *********************** 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 409 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.382 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: A 64 LYS cc_start: 0.6729 (tppt) cc_final: 0.6084 (ttmm) REVERT: A 180 THR cc_start: 0.7618 (p) cc_final: 0.7305 (p) REVERT: A 183 MET cc_start: 0.6345 (mmp) cc_final: 0.5654 (mmp) REVERT: A 201 MET cc_start: 0.7939 (mtt) cc_final: 0.7715 (mtt) REVERT: A 215 ASP cc_start: 0.8628 (m-30) cc_final: 0.8411 (m-30) REVERT: A 312 ILE cc_start: 0.8109 (tt) cc_final: 0.7757 (tt) REVERT: A 343 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 38 LYS cc_start: 0.7755 (tptt) cc_final: 0.7394 (tppt) REVERT: B 52 GLN cc_start: 0.8022 (mm110) cc_final: 0.7814 (mm110) REVERT: B 133 GLU cc_start: 0.8737 (mp0) cc_final: 0.8446 (tm-30) REVERT: B 211 GLN cc_start: 0.9236 (pm20) cc_final: 0.9024 (pm20) REVERT: B 237 LEU cc_start: 0.9230 (mm) cc_final: 0.8894 (tp) REVERT: B 334 LYS cc_start: 0.7748 (tttm) cc_final: 0.7473 (tttm) REVERT: B 380 ILE cc_start: 0.7960 (mm) cc_final: 0.7722 (mm) REVERT: C 72 SER cc_start: 0.7970 (p) cc_final: 0.7737 (t) REVERT: C 375 ASP cc_start: 0.8679 (m-30) cc_final: 0.8253 (t0) REVERT: C 394 LYS cc_start: 0.8768 (mptt) cc_final: 0.8413 (tmtt) REVERT: D 37 MET cc_start: 0.7584 (tpt) cc_final: 0.7357 (tpt) REVERT: D 41 LEU cc_start: 0.9382 (tp) cc_final: 0.9175 (tp) REVERT: D 52 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6015 (tttt) REVERT: D 64 ILE cc_start: 0.8369 (mm) cc_final: 0.8161 (mm) REVERT: D 136 MET cc_start: 0.3590 (tmm) cc_final: 0.3334 (tmm) REVERT: E 7 ASN cc_start: 0.8868 (t0) cc_final: 0.8651 (t0) REVERT: E 37 MET cc_start: 0.8060 (mmp) cc_final: 0.6818 (mtm) REVERT: E 122 ARG cc_start: 0.4270 (ttt180) cc_final: 0.2915 (mmt180) REVERT: E 129 ARG cc_start: 0.8045 (ttm170) cc_final: 0.7684 (ttm-80) REVERT: F 37 MET cc_start: 0.7186 (ttp) cc_final: 0.6886 (ttm) REVERT: F 47 ASP cc_start: 0.8304 (m-30) cc_final: 0.8019 (m-30) REVERT: F 63 ASP cc_start: 0.6746 (t0) cc_final: 0.6405 (t0) REVERT: F 133 PHE cc_start: 0.5985 (m-80) cc_final: 0.5754 (m-80) REVERT: F 136 MET cc_start: 0.7212 (ptm) cc_final: 0.6770 (ppp) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.5421 time to fit residues: 331.5948 Evaluate side-chains 362 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.163698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128702 restraints weight = 111033.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134759 restraints weight = 51388.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138745 restraints weight = 30084.845| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 15695 Z= 0.196 Angle : 0.695 28.649 21250 Z= 0.366 Chirality : 0.044 0.304 2418 Planarity : 0.005 0.151 2670 Dihedral : 5.717 32.176 2091 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.86 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.18), residues: 1971 helix: 0.76 (0.24), residues: 448 sheet: -1.45 (0.22), residues: 517 loop : -2.17 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 74 HIS 0.005 0.001 HIS E 130 PHE 0.023 0.001 PHE F 155 TYR 0.012 0.002 TYR F 51 ARG 0.009 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 629) hydrogen bonds : angle 5.83187 ( 1704) SS BOND : bond 0.00964 ( 26) SS BOND : angle 3.60073 ( 52) covalent geometry : bond 0.00441 (15669) covalent geometry : angle 0.67262 (21198) *********************** 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 : 2.351 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 180 THR cc_start: 0.7754 (p) cc_final: 0.7419 (p) REVERT: A 183 MET cc_start: 0.6444 (mmp) cc_final: 0.5629 (mmp) REVERT: A 215 ASP cc_start: 0.8613 (m-30) cc_final: 0.8409 (m-30) REVERT: A 312 ILE cc_start: 0.7913 (tt) cc_final: 0.7600 (tt) REVERT: A 343 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 401 MET cc_start: 0.8284 (mmm) cc_final: 0.8015 (mmm) REVERT: B 30 CYS cc_start: 0.3991 (t) cc_final: 0.3780 (t) REVERT: B 34 MET cc_start: 0.8575 (mtt) cc_final: 0.8080 (mtt) REVERT: B 38 LYS cc_start: 0.7769 (tptt) cc_final: 0.7451 (tppt) REVERT: B 52 GLN cc_start: 0.8064 (mm110) cc_final: 0.7844 (mm110) REVERT: B 133 GLU cc_start: 0.8709 (mp0) cc_final: 0.8422 (tm-30) REVERT: B 237 LEU cc_start: 0.9109 (mm) cc_final: 0.8840 (tp) REVERT: B 334 LYS cc_start: 0.7621 (tttm) cc_final: 0.7357 (tttm) REVERT: C 42 ASP cc_start: 0.7264 (t0) cc_final: 0.6761 (t0) REVERT: C 137 TYR cc_start: 0.8078 (m-80) cc_final: 0.7640 (m-80) REVERT: C 375 ASP cc_start: 0.8577 (m-30) cc_final: 0.8187 (t0) REVERT: C 394 LYS cc_start: 0.8746 (mptt) cc_final: 0.8419 (tmtt) REVERT: C 448 PHE cc_start: 0.7397 (m-10) cc_final: 0.6968 (m-10) REVERT: D 41 LEU cc_start: 0.9356 (tp) cc_final: 0.9150 (tp) REVERT: D 49 ILE cc_start: 0.7671 (mm) cc_final: 0.7344 (tp) REVERT: D 52 LYS cc_start: 0.7169 (mmmm) cc_final: 0.5885 (tttt) REVERT: D 136 MET cc_start: 0.3501 (tmm) cc_final: 0.3242 (tmm) REVERT: E 7 ASN cc_start: 0.8867 (t0) cc_final: 0.8659 (t0) REVERT: E 37 MET cc_start: 0.7974 (mmp) cc_final: 0.6836 (mtp) REVERT: E 56 LEU cc_start: 0.8369 (mm) cc_final: 0.7643 (tt) REVERT: E 122 ARG cc_start: 0.4273 (ttt180) cc_final: 0.2902 (mmt180) REVERT: E 129 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7686 (ttm-80) REVERT: F 37 MET cc_start: 0.7142 (ttp) cc_final: 0.6743 (ttm) REVERT: F 47 ASP cc_start: 0.8321 (m-30) cc_final: 0.8071 (m-30) REVERT: F 63 ASP cc_start: 0.6879 (t0) cc_final: 0.6540 (t0) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.5389 time to fit residues: 338.7367 Evaluate side-chains 358 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 106 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.178082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.142520 restraints weight = 108491.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.148688 restraints weight = 48467.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.152720 restraints weight = 27861.465| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 15695 Z= 0.234 Angle : 0.722 28.004 21250 Z= 0.381 Chirality : 0.044 0.333 2418 Planarity : 0.005 0.084 2670 Dihedral : 5.758 30.819 2091 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.54 % Favored : 90.26 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1971 helix: 0.77 (0.24), residues: 448 sheet: -1.41 (0.22), residues: 516 loop : -2.29 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 220 HIS 0.007 0.001 HIS A 144 PHE 0.024 0.002 PHE F 155 TYR 0.013 0.002 TYR F 51 ARG 0.010 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 629) hydrogen bonds : angle 5.75521 ( 1704) SS BOND : bond 0.00701 ( 26) SS BOND : angle 3.56244 ( 52) covalent geometry : bond 0.00512 (15669) covalent geometry : angle 0.70137 (21198) *********************** 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 408 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 2.447 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: A 180 THR cc_start: 0.7910 (p) cc_final: 0.7566 (p) REVERT: A 201 MET cc_start: 0.8121 (mtt) cc_final: 0.7822 (mtt) REVERT: A 215 ASP cc_start: 0.8656 (m-30) cc_final: 0.8446 (m-30) REVERT: A 312 ILE cc_start: 0.8121 (tt) cc_final: 0.7801 (tt) REVERT: A 343 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 386 GLN cc_start: 0.6830 (tp40) cc_final: 0.6511 (pm20) REVERT: A 401 MET cc_start: 0.8228 (mmm) cc_final: 0.7943 (mmm) REVERT: B 34 MET cc_start: 0.8576 (mtt) cc_final: 0.8234 (mtt) REVERT: B 125 MET cc_start: 0.7650 (mmm) cc_final: 0.5892 (mmt) REVERT: B 133 GLU cc_start: 0.8725 (mp0) cc_final: 0.8419 (tm-30) REVERT: B 237 LEU cc_start: 0.9201 (mm) cc_final: 0.8853 (tp) REVERT: B 334 LYS cc_start: 0.7693 (tttm) cc_final: 0.7432 (tttm) REVERT: C 42 ASP cc_start: 0.7303 (t0) cc_final: 0.6812 (t0) REVERT: C 137 TYR cc_start: 0.8194 (m-80) cc_final: 0.7747 (m-80) REVERT: C 283 LEU cc_start: 0.8671 (tp) cc_final: 0.8421 (tp) REVERT: C 375 ASP cc_start: 0.8647 (m-30) cc_final: 0.7801 (t0) REVERT: C 392 PHE cc_start: 0.8287 (t80) cc_final: 0.7287 (t80) REVERT: C 448 PHE cc_start: 0.7471 (m-10) cc_final: 0.7043 (m-10) REVERT: D 37 MET cc_start: 0.7231 (tpt) cc_final: 0.6925 (tpt) REVERT: D 41 LEU cc_start: 0.9404 (tp) cc_final: 0.9192 (tp) REVERT: D 52 LYS cc_start: 0.7220 (mmmm) cc_final: 0.5899 (tttp) REVERT: D 136 MET cc_start: 0.3444 (tmm) cc_final: 0.3192 (tmm) REVERT: E 7 ASN cc_start: 0.8967 (t0) cc_final: 0.8730 (t0) REVERT: E 37 MET cc_start: 0.7871 (mmp) cc_final: 0.6569 (mtp) REVERT: E 129 ARG cc_start: 0.8023 (ttm170) cc_final: 0.7692 (ttm-80) REVERT: F 37 MET cc_start: 0.7337 (ttp) cc_final: 0.6760 (ttm) REVERT: F 47 ASP cc_start: 0.8380 (m-30) cc_final: 0.8104 (m-30) REVERT: F 63 ASP cc_start: 0.7040 (t0) cc_final: 0.6687 (t0) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.5674 time to fit residues: 351.3084 Evaluate side-chains 351 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 172 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.165258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130953 restraints weight = 105740.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136999 restraints weight = 48777.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140982 restraints weight = 28416.744| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 15695 Z= 0.148 Angle : 0.681 29.687 21250 Z= 0.354 Chirality : 0.045 0.345 2418 Planarity : 0.005 0.180 2670 Dihedral : 5.584 30.215 2091 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.95 % Favored : 92.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 1971 helix: 0.89 (0.24), residues: 449 sheet: -1.33 (0.22), residues: 517 loop : -2.10 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 391 HIS 0.009 0.001 HIS A 144 PHE 0.024 0.001 PHE F 155 TYR 0.011 0.001 TYR C 299 ARG 0.008 0.001 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 629) hydrogen bonds : angle 5.57885 ( 1704) SS BOND : bond 0.00871 ( 26) SS BOND : angle 3.63701 ( 52) covalent geometry : bond 0.00362 (15669) covalent geometry : angle 0.65740 (21198) *********************** 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 423 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 2.375 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: A 158 HIS cc_start: 0.5638 (m-70) cc_final: 0.5405 (m-70) REVERT: A 180 THR cc_start: 0.7859 (p) cc_final: 0.7509 (p) REVERT: A 201 MET cc_start: 0.7944 (mtt) cc_final: 0.7720 (mtt) REVERT: A 260 MET cc_start: 0.8539 (mmt) cc_final: 0.8279 (mmt) REVERT: A 343 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8228 (tm-30) REVERT: A 392 PHE cc_start: 0.8447 (t80) cc_final: 0.8065 (t80) REVERT: A 401 MET cc_start: 0.8170 (mmm) cc_final: 0.7882 (mmm) REVERT: B 34 MET cc_start: 0.8515 (mtt) cc_final: 0.8158 (mtt) REVERT: B 38 LYS cc_start: 0.8151 (tptt) cc_final: 0.7689 (tppt) REVERT: B 125 MET cc_start: 0.7639 (mmm) cc_final: 0.6491 (mmt) REVERT: B 133 GLU cc_start: 0.8701 (mp0) cc_final: 0.8356 (tm-30) REVERT: B 201 MET cc_start: 0.7694 (mtm) cc_final: 0.6892 (mtm) REVERT: B 237 LEU cc_start: 0.9023 (mm) cc_final: 0.8766 (tp) REVERT: B 260 MET cc_start: 0.8496 (mmp) cc_final: 0.8041 (mmm) REVERT: B 303 THR cc_start: 0.8013 (p) cc_final: 0.7726 (t) REVERT: B 334 LYS cc_start: 0.7584 (tttm) cc_final: 0.7340 (tttm) REVERT: B 380 ILE cc_start: 0.7998 (mm) cc_final: 0.7782 (mm) REVERT: C 42 ASP cc_start: 0.6964 (t0) cc_final: 0.6578 (t0) REVERT: C 137 TYR cc_start: 0.8088 (m-80) cc_final: 0.7699 (m-80) REVERT: C 283 LEU cc_start: 0.8642 (tp) cc_final: 0.8422 (tp) REVERT: C 375 ASP cc_start: 0.8660 (m-30) cc_final: 0.7853 (t0) REVERT: C 392 PHE cc_start: 0.8258 (t80) cc_final: 0.7456 (t80) REVERT: C 448 PHE cc_start: 0.7398 (m-10) cc_final: 0.6979 (m-10) REVERT: D 37 MET cc_start: 0.7135 (tpt) cc_final: 0.6782 (tpt) REVERT: D 52 LYS cc_start: 0.6972 (mmmm) cc_final: 0.5681 (tttp) REVERT: D 136 MET cc_start: 0.3479 (tmm) cc_final: 0.3239 (tmm) REVERT: E 7 ASN cc_start: 0.8930 (t0) cc_final: 0.8697 (t0) REVERT: E 37 MET cc_start: 0.7813 (mmp) cc_final: 0.6433 (mtp) REVERT: E 56 LEU cc_start: 0.8484 (mm) cc_final: 0.7635 (tt) REVERT: E 129 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7683 (ttm-80) REVERT: F 37 MET cc_start: 0.7245 (ttp) cc_final: 0.6664 (ttm) REVERT: F 47 ASP cc_start: 0.8331 (m-30) cc_final: 0.8103 (m-30) REVERT: F 63 ASP cc_start: 0.6999 (t0) cc_final: 0.6673 (t0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.5415 time to fit residues: 345.1437 Evaluate side-chains 365 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 38 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 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 = 0.4213 r_free = 0.4213 target = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132400 restraints weight = 109747.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138363 restraints weight = 52375.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142198 restraints weight = 31099.135| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 15695 Z= 0.144 Angle : 0.674 30.331 21250 Z= 0.351 Chirality : 0.044 0.352 2418 Planarity : 0.005 0.118 2670 Dihedral : 5.421 31.541 2091 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.00 % Favored : 92.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 1971 helix: 0.96 (0.24), residues: 449 sheet: -1.24 (0.23), residues: 506 loop : -2.03 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 20 HIS 0.008 0.001 HIS C 282 PHE 0.026 0.001 PHE C 306 TYR 0.009 0.001 TYR C 326 ARG 0.008 0.001 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 629) hydrogen bonds : angle 5.44409 ( 1704) SS BOND : bond 0.00991 ( 26) SS BOND : angle 3.66655 ( 52) covalent geometry : bond 0.00351 (15669) covalent geometry : angle 0.65009 (21198) *********************** 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 418 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 2.486 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 158 HIS cc_start: 0.5590 (m-70) cc_final: 0.5388 (m-70) REVERT: A 260 MET cc_start: 0.8552 (mmt) cc_final: 0.8348 (mmt) REVERT: A 272 MET cc_start: 0.8844 (ppp) cc_final: 0.8630 (ppp) REVERT: A 282 HIS cc_start: 0.8368 (m90) cc_final: 0.7811 (m90) REVERT: A 343 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 401 MET cc_start: 0.8130 (mmm) cc_final: 0.7864 (mmm) REVERT: B 34 MET cc_start: 0.8498 (mtt) cc_final: 0.8089 (mtt) REVERT: B 38 LYS cc_start: 0.8138 (tptt) cc_final: 0.7699 (tppt) REVERT: B 133 GLU cc_start: 0.8610 (mp0) cc_final: 0.8318 (tm-30) REVERT: B 237 LEU cc_start: 0.9150 (mm) cc_final: 0.8717 (tp) REVERT: B 303 THR cc_start: 0.7971 (p) cc_final: 0.7687 (t) REVERT: B 334 LYS cc_start: 0.7446 (tttm) cc_final: 0.7240 (tttm) REVERT: B 380 ILE cc_start: 0.8136 (mm) cc_final: 0.7899 (mm) REVERT: C 42 ASP cc_start: 0.6647 (t0) cc_final: 0.6338 (t0) REVERT: C 137 TYR cc_start: 0.8018 (m-80) cc_final: 0.7682 (m-80) REVERT: C 288 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7699 (mtp-110) REVERT: C 375 ASP cc_start: 0.8427 (m-30) cc_final: 0.7755 (t0) REVERT: C 392 PHE cc_start: 0.7898 (t80) cc_final: 0.7283 (t80) REVERT: C 448 PHE cc_start: 0.7381 (m-10) cc_final: 0.6971 (m-10) REVERT: D 37 MET cc_start: 0.6947 (tpt) cc_final: 0.6629 (tpt) REVERT: D 41 LEU cc_start: 0.9324 (tp) cc_final: 0.9102 (tp) REVERT: D 52 LYS cc_start: 0.6790 (mmmm) cc_final: 0.5418 (tttp) REVERT: D 136 MET cc_start: 0.3457 (tmm) cc_final: 0.3225 (tmm) REVERT: E 7 ASN cc_start: 0.8933 (t0) cc_final: 0.8721 (t0) REVERT: E 37 MET cc_start: 0.7641 (mmp) cc_final: 0.6461 (mtp) REVERT: E 56 LEU cc_start: 0.8468 (mm) cc_final: 0.7657 (tt) REVERT: E 129 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7685 (ttm-80) REVERT: F 37 MET cc_start: 0.7052 (ttp) cc_final: 0.6533 (ttm) REVERT: F 63 ASP cc_start: 0.7041 (t0) cc_final: 0.6677 (t0) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.5321 time to fit residues: 336.9859 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 : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 94 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.166950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133251 restraints weight = 106535.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139281 restraints weight = 49228.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143265 restraints weight = 28633.971| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 15695 Z= 0.143 Angle : 0.678 31.406 21250 Z= 0.351 Chirality : 0.045 0.363 2418 Planarity : 0.004 0.107 2670 Dihedral : 5.333 30.333 2091 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.24 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1971 helix: 1.02 (0.24), residues: 450 sheet: -1.16 (0.23), residues: 512 loop : -1.95 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 391 HIS 0.013 0.001 HIS B 261 PHE 0.024 0.001 PHE F 155 TYR 0.010 0.001 TYR A 326 ARG 0.017 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 629) hydrogen bonds : angle 5.37289 ( 1704) SS BOND : bond 0.00975 ( 26) SS BOND : angle 3.73330 ( 52) covalent geometry : bond 0.00351 (15669) covalent geometry : angle 0.65286 (21198) *********************** 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 420 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 2.734 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 158 HIS cc_start: 0.5658 (m-70) cc_final: 0.5240 (m-70) REVERT: A 183 MET cc_start: 0.6747 (mmp) cc_final: 0.5859 (mmp) REVERT: A 282 HIS cc_start: 0.8431 (m90) cc_final: 0.7851 (m90) REVERT: A 343 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 373 PHE cc_start: 0.7950 (m-80) cc_final: 0.7684 (m-80) REVERT: A 392 PHE cc_start: 0.8392 (t80) cc_final: 0.7952 (t80) REVERT: A 401 MET cc_start: 0.8204 (mmm) cc_final: 0.7921 (mmm) REVERT: B 38 LYS cc_start: 0.8108 (tptt) cc_final: 0.7711 (tppt) REVERT: B 133 GLU cc_start: 0.8646 (mp0) cc_final: 0.8293 (tm-30) REVERT: B 237 LEU cc_start: 0.9091 (mm) cc_final: 0.8724 (tp) REVERT: B 303 THR cc_start: 0.7940 (p) cc_final: 0.7724 (t) REVERT: B 380 ILE cc_start: 0.7969 (mm) cc_final: 0.7722 (mm) REVERT: C 42 ASP cc_start: 0.6812 (t0) cc_final: 0.6492 (t0) REVERT: C 137 TYR cc_start: 0.8019 (m-80) cc_final: 0.7636 (m-80) REVERT: C 283 LEU cc_start: 0.8594 (tp) cc_final: 0.8382 (tp) REVERT: C 375 ASP cc_start: 0.8632 (m-30) cc_final: 0.7826 (t0) REVERT: C 392 PHE cc_start: 0.7976 (t80) cc_final: 0.7402 (t80) REVERT: C 448 PHE cc_start: 0.7404 (m-10) cc_final: 0.6977 (m-10) REVERT: D 41 LEU cc_start: 0.9406 (tp) cc_final: 0.9172 (tp) REVERT: D 52 LYS cc_start: 0.6827 (mmmm) cc_final: 0.5522 (tttp) REVERT: D 136 MET cc_start: 0.3387 (tmm) cc_final: 0.3129 (tmm) REVERT: E 7 ASN cc_start: 0.8947 (t0) cc_final: 0.8710 (t0) REVERT: E 37 MET cc_start: 0.7748 (mmp) cc_final: 0.7536 (mmp) REVERT: E 56 LEU cc_start: 0.8470 (mm) cc_final: 0.7583 (tt) REVERT: E 129 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7673 (ttm-80) REVERT: F 25 PHE cc_start: 0.4685 (p90) cc_final: 0.4181 (p90) REVERT: F 37 MET cc_start: 0.7213 (ttp) cc_final: 0.6665 (ttm) REVERT: F 47 ASP cc_start: 0.8249 (m-30) cc_final: 0.8037 (m-30) REVERT: F 63 ASP cc_start: 0.6964 (t0) cc_final: 0.6582 (t0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.5242 time to fit residues: 335.1831 Evaluate side-chains 366 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 74 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4394 r_free = 0.4394 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137840 restraints weight = 107888.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.143857 restraints weight = 48521.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.147825 restraints weight = 27844.856| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 15695 Z= 0.200 Angle : 0.710 31.940 21250 Z= 0.369 Chirality : 0.044 0.364 2418 Planarity : 0.005 0.099 2670 Dihedral : 5.402 29.652 2091 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.52 % Favored : 91.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1971 helix: 0.93 (0.24), residues: 450 sheet: -1.19 (0.23), residues: 510 loop : -2.10 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 220 HIS 0.006 0.001 HIS B 261 PHE 0.024 0.002 PHE F 155 TYR 0.012 0.002 TYR B 444 ARG 0.011 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 629) hydrogen bonds : angle 5.37532 ( 1704) SS BOND : bond 0.01012 ( 26) SS BOND : angle 3.84268 ( 52) covalent geometry : bond 0.00464 (15669) covalent geometry : angle 0.68451 (21198) ********************** 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 412 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.460 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: 0.5776 (m-70) cc_final: 0.5397 (m-70) REVERT: A 343 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 401 MET cc_start: 0.8209 (mmm) cc_final: 0.7916 (mmm) REVERT: B 38 LYS cc_start: 0.8147 (tptt) cc_final: 0.7723 (tppt) REVERT: B 133 GLU cc_start: 0.8682 (mp0) cc_final: 0.8322 (tm-30) REVERT: B 237 LEU cc_start: 0.9138 (mm) cc_final: 0.8791 (tp) REVERT: B 303 THR cc_start: 0.7933 (p) cc_final: 0.7702 (t) REVERT: C 42 ASP cc_start: 0.7155 (t0) cc_final: 0.6714 (t0) REVERT: C 137 TYR cc_start: 0.8173 (m-80) cc_final: 0.7741 (m-80) REVERT: C 283 LEU cc_start: 0.8671 (tp) cc_final: 0.8412 (tp) REVERT: C 375 ASP cc_start: 0.8651 (m-30) cc_final: 0.7834 (t0) REVERT: C 392 PHE cc_start: 0.8160 (t80) cc_final: 0.7575 (t80) REVERT: D 37 MET cc_start: 0.7064 (tpt) cc_final: 0.6728 (tpt) REVERT: D 136 MET cc_start: 0.3366 (tmm) cc_final: 0.3111 (tmm) REVERT: E 7 ASN cc_start: 0.8978 (t0) cc_final: 0.8737 (t0) REVERT: E 37 MET cc_start: 0.7707 (mmp) cc_final: 0.7313 (mmp) REVERT: E 56 LEU cc_start: 0.8506 (mm) cc_final: 0.7674 (tt) REVERT: E 129 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7678 (ttm-80) REVERT: F 37 MET cc_start: 0.7197 (ttp) cc_final: 0.6615 (ttm) REVERT: F 47 ASP cc_start: 0.8297 (m-30) cc_final: 0.8008 (m-30) REVERT: F 63 ASP cc_start: 0.6957 (t0) cc_final: 0.6589 (t0) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.5495 time to fit residues: 344.5962 Evaluate side-chains 359 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 152 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 386 GLN B 437 HIS ** F 59 ASN ** 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 = 0.4422 r_free = 0.4422 target = 0.174207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.140147 restraints weight = 107725.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.146333 restraints weight = 47833.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.150331 restraints weight = 27219.279| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 15695 Z= 0.149 Angle : 0.683 31.163 21250 Z= 0.353 Chirality : 0.044 0.337 2418 Planarity : 0.004 0.101 2670 Dihedral : 5.319 29.417 2091 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.65 % Favored : 93.15 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1971 helix: 1.02 (0.24), residues: 450 sheet: -1.10 (0.23), residues: 517 loop : -2.00 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 220 HIS 0.006 0.001 HIS B 437 PHE 0.025 0.001 PHE F 155 TYR 0.012 0.001 TYR F 77 ARG 0.011 0.001 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 629) hydrogen bonds : angle 5.30672 ( 1704) SS BOND : bond 0.01152 ( 26) SS BOND : angle 3.79419 ( 52) covalent geometry : bond 0.00363 (15669) covalent geometry : angle 0.65733 (21198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.49 seconds wall clock time: 186 minutes 2.20 seconds (11162.20 seconds total)