Starting phenix.real_space_refine on Thu Jun 26 18:31:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dof_47082/06_2025/9dof_47082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dof_47082/06_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_47082/06_2025/9dof_47082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dof_47082/06_2025/9dof_47082.map" model { file = "/net/cci-nas-00/data/ceres_data/9dof_47082/06_2025/9dof_47082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dof_47082/06_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-5710/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: 13.39, per 1000 atoms: 0.44 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: 7.16 Conformation dependent library (CDL) restraints added in 2.5 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: 2.66 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: 11.70 Time building geometry restraints manager: 8.88 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: 1.430 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: 0.490 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 61.180 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- 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 : 2.432 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: 0.5403 time to fit residues: 350.7779 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 : 2.274 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.151830 restraints weight = 109341.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.158221 restraints weight = 48624.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.162334 restraints weight = 27609.586| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- 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 30.048 21250 Z= 0.371 Chirality : 0.044 0.320 2418 Planarity : 0.005 0.059 2670 Dihedral : 5.835 38.556 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 0.007 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 629) hydrogen bonds : angle 6.32697 ( 1704) SS BOND : bond 0.00883 ( 26) SS BOND : angle 3.76710 ( 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 : 2.375 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: symmetry clash REVERT: A 64 LYS cc_start: 0.6392 (tppt) cc_final: 0.5749 (ttmm) REVERT: A 103 ASN cc_start: 0.7258 (m110) cc_final: 0.6933 (m110) REVERT: A 183 MET cc_start: 0.6143 (mmp) cc_final: 0.5708 (mmp) REVERT: A 196 MET cc_start: 0.8401 (ptm) cc_final: 0.8154 (ptm) REVERT: A 312 ILE cc_start: 0.8001 (tt) cc_final: 0.7745 (tt) REVERT: A 343 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 350 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6636 (ttp-110) REVERT: A 453 TRP cc_start: 0.6170 (p-90) cc_final: 0.5916 (p-90) REVERT: B 125 MET cc_start: 0.6532 (mmt) cc_final: 0.4907 (mmt) REVERT: B 133 GLU cc_start: 0.8609 (mp0) cc_final: 0.8325 (tm-30) REVERT: B 201 MET cc_start: 0.7375 (mtp) cc_final: 0.6813 (mtp) REVERT: B 237 LEU cc_start: 0.9259 (mm) cc_final: 0.8773 (tp) REVERT: B 334 LYS cc_start: 0.7554 (tttm) cc_final: 0.7252 (tttm) REVERT: C 42 ASP cc_start: 0.7354 (t0) cc_final: 0.6816 (t0) REVERT: C 118 MET cc_start: 0.5922 (tpt) cc_final: 0.5715 (tpt) REVERT: C 375 ASP cc_start: 0.8710 (m-30) cc_final: 0.8231 (t0) REVERT: C 394 LYS cc_start: 0.8956 (mmtm) cc_final: 0.7817 (tmtt) REVERT: D 49 ILE cc_start: 0.7618 (mm) cc_final: 0.7346 (tp) REVERT: D 64 ILE cc_start: 0.8431 (mm) cc_final: 0.8205 (mm) REVERT: D 136 MET cc_start: 0.3429 (tmm) cc_final: 0.3162 (tmm) REVERT: E 35 THR cc_start: 0.8277 (m) cc_final: 0.8068 (m) REVERT: E 37 MET cc_start: 0.7935 (mmp) cc_final: 0.6742 (mtm) REVERT: E 122 ARG cc_start: 0.4441 (ttt180) cc_final: 0.2880 (mmt180) REVERT: E 129 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7663 (ttm-80) REVERT: F 47 ASP cc_start: 0.8199 (m-30) cc_final: 0.7837 (m-30) REVERT: F 63 ASP cc_start: 0.6374 (t0) cc_final: 0.6038 (t0) outliers start: 2 outliers final: 1 residues processed: 423 average time/residue: 0.6106 time to fit residues: 393.1707 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 : 2.504 ------------------------------------------------------------------------------- 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: 0.8980 chunk 166 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.185962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.151272 restraints weight = 110078.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.157704 restraints weight = 48678.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.161865 restraints weight = 27547.302| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 15695 Z= 0.165 Angle : 0.682 30.385 21250 Z= 0.356 Chirality : 0.044 0.307 2418 Planarity : 0.005 0.129 2670 Dihedral : 5.652 34.356 2091 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.46 % Favored : 92.34 % Rotamer: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % 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: -1.80 (0.18), residues: 1971 helix: 0.65 (0.24), residues: 444 sheet: -1.49 (0.22), residues: 502 loop : -1.89 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.006 0.001 HIS C 94 PHE 0.023 0.001 PHE F 155 TYR 0.009 0.001 TYR C 299 ARG 0.008 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 629) hydrogen bonds : angle 6.02698 ( 1704) SS BOND : bond 0.00826 ( 26) SS BOND : angle 3.63234 ( 52) covalent geometry : bond 0.00382 (15669) covalent geometry : angle 0.65841 (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 424 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6525 (tppt) cc_final: 0.5892 (ttmm) REVERT: A 103 ASN cc_start: 0.7305 (m110) cc_final: 0.7066 (m110) REVERT: A 180 THR cc_start: 0.7376 (p) cc_final: 0.7087 (p) REVERT: A 183 MET cc_start: 0.6078 (mmp) cc_final: 0.5539 (mmp) REVERT: A 196 MET cc_start: 0.8376 (ptm) cc_final: 0.8128 (ptm) REVERT: A 312 ILE cc_start: 0.8004 (tt) cc_final: 0.7730 (tt) REVERT: A 343 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 350 ARG cc_start: 0.7010 (ttp-110) cc_final: 0.6772 (ttp-110) REVERT: A 453 TRP cc_start: 0.6116 (p-90) cc_final: 0.5834 (p-90) REVERT: B 38 LYS cc_start: 0.7560 (tptt) cc_final: 0.7225 (tppt) REVERT: B 133 GLU cc_start: 0.8626 (mp0) cc_final: 0.8337 (tm-30) REVERT: B 237 LEU cc_start: 0.9050 (mm) cc_final: 0.8670 (tp) REVERT: B 260 MET cc_start: 0.8244 (mmp) cc_final: 0.7998 (mmm) REVERT: B 334 LYS cc_start: 0.7673 (tttm) cc_final: 0.7382 (tttm) REVERT: C 42 ASP cc_start: 0.7353 (t0) cc_final: 0.6789 (t0) REVERT: C 92 CYS cc_start: 0.2840 (p) cc_final: 0.2546 (p) REVERT: C 375 ASP cc_start: 0.8688 (m-30) cc_final: 0.8220 (t0) REVERT: C 394 LYS cc_start: 0.8773 (mptt) cc_final: 0.8241 (tmtt) REVERT: D 37 MET cc_start: 0.7252 (tpt) cc_final: 0.6733 (tpt) REVERT: D 49 ILE cc_start: 0.7623 (mm) cc_final: 0.7328 (tp) REVERT: D 52 LYS cc_start: 0.6709 (mmmm) cc_final: 0.5235 (tttt) REVERT: D 64 ILE cc_start: 0.8561 (mm) cc_final: 0.8347 (mm) REVERT: D 136 MET cc_start: 0.3471 (tmm) cc_final: 0.3238 (tmm) REVERT: E 37 MET cc_start: 0.7796 (mmp) cc_final: 0.6347 (mtp) REVERT: E 56 LEU cc_start: 0.8226 (mm) cc_final: 0.7422 (tt) REVERT: E 122 ARG cc_start: 0.4373 (ttt180) cc_final: 0.2833 (mmt180) REVERT: E 129 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7643 (ttm-80) REVERT: F 47 ASP cc_start: 0.8248 (m-30) cc_final: 0.7916 (m-30) REVERT: F 63 ASP cc_start: 0.6466 (t0) cc_final: 0.6111 (t0) outliers start: 1 outliers final: 1 residues processed: 423 average time/residue: 0.5503 time to fit residues: 350.7886 Evaluate side-chains 377 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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: 0.3980 chunk 173 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 244 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.163356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128221 restraints weight = 110503.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134229 restraints weight = 51354.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138178 restraints weight = 30157.532| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 15695 Z= 0.255 Angle : 0.726 28.726 21250 Z= 0.385 Chirality : 0.044 0.337 2418 Planarity : 0.005 0.101 2670 Dihedral : 5.758 32.214 2091 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.93 (0.18), residues: 1971 helix: 0.70 (0.24), residues: 446 sheet: -1.48 (0.22), residues: 518 loop : -2.12 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 74 HIS 0.005 0.001 HIS E 130 PHE 0.024 0.002 PHE F 155 TYR 0.013 0.002 TYR A 444 ARG 0.016 0.001 ARG D 6 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 629) hydrogen bonds : angle 5.96667 ( 1704) SS BOND : bond 0.01070 ( 26) SS BOND : angle 3.54293 ( 52) covalent geometry : bond 0.00550 (15669) covalent geometry : angle 0.70535 (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 414 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 2.325 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: A 64 LYS cc_start: 0.6786 (tppt) cc_final: 0.6159 (ttmm) REVERT: A 180 THR cc_start: 0.7495 (p) cc_final: 0.7165 (p) REVERT: A 183 MET cc_start: 0.6178 (mmp) cc_final: 0.5559 (mmp) REVERT: A 201 MET cc_start: 0.7850 (mtt) cc_final: 0.7639 (mtt) REVERT: A 215 ASP cc_start: 0.8595 (m-30) cc_final: 0.8383 (m-30) REVERT: A 312 ILE cc_start: 0.8077 (tt) cc_final: 0.7723 (tt) REVERT: A 343 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 30 CYS cc_start: 0.3887 (t) cc_final: 0.3687 (t) REVERT: B 38 LYS cc_start: 0.7756 (tptt) cc_final: 0.7397 (tppt) REVERT: B 52 GLN cc_start: 0.8021 (mm110) cc_final: 0.7820 (mm110) REVERT: B 133 GLU cc_start: 0.8712 (mp0) cc_final: 0.8454 (tm-30) REVERT: B 211 GLN cc_start: 0.9190 (pm20) cc_final: 0.8958 (pm20) REVERT: B 237 LEU cc_start: 0.9206 (mm) cc_final: 0.8860 (tp) REVERT: B 334 LYS cc_start: 0.7714 (tttm) cc_final: 0.7456 (tttm) REVERT: C 72 SER cc_start: 0.7948 (p) cc_final: 0.7742 (t) REVERT: C 375 ASP cc_start: 0.8567 (m-30) cc_final: 0.8164 (t0) REVERT: C 394 LYS cc_start: 0.8752 (mptt) cc_final: 0.8429 (tmtt) REVERT: D 37 MET cc_start: 0.7371 (tpt) cc_final: 0.7159 (tpt) REVERT: D 52 LYS cc_start: 0.7069 (mmmm) cc_final: 0.5998 (tttt) REVERT: D 64 ILE cc_start: 0.8313 (mm) cc_final: 0.8104 (mm) REVERT: D 136 MET cc_start: 0.3616 (tmm) cc_final: 0.3356 (tmm) REVERT: E 37 MET cc_start: 0.7981 (mmp) cc_final: 0.6746 (mtm) REVERT: E 122 ARG cc_start: 0.4298 (ttt180) cc_final: 0.2933 (mmt180) REVERT: E 129 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7699 (ttm-80) REVERT: F 37 MET cc_start: 0.7105 (ttp) cc_final: 0.6845 (ttm) REVERT: F 47 ASP cc_start: 0.8252 (m-30) cc_final: 0.7998 (m-30) REVERT: F 63 ASP cc_start: 0.6722 (t0) cc_final: 0.6415 (t0) REVERT: F 133 PHE cc_start: 0.6047 (m-80) cc_final: 0.5822 (m-80) REVERT: F 136 MET cc_start: 0.7227 (ptm) cc_final: 0.6764 (ppp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.5421 time to fit residues: 338.1878 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 : 2.317 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 HIS B 437 HIS C 94 HIS C 256 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.165810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131091 restraints weight = 107013.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137120 restraints weight = 49621.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141055 restraints weight = 29032.850| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 15695 Z= 0.173 Angle : 0.682 28.826 21250 Z= 0.358 Chirality : 0.044 0.323 2418 Planarity : 0.005 0.157 2670 Dihedral : 5.649 32.188 2091 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.66 % Favored : 92.14 % 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: -1.84 (0.18), residues: 1971 helix: 0.79 (0.24), residues: 448 sheet: -1.39 (0.22), residues: 507 loop : -2.09 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.008 0.001 HIS A 144 PHE 0.023 0.001 PHE F 155 TYR 0.011 0.002 TYR F 51 ARG 0.008 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 629) hydrogen bonds : angle 5.79914 ( 1704) SS BOND : bond 0.01079 ( 26) SS BOND : angle 3.55237 ( 52) covalent geometry : bond 0.00399 (15669) covalent geometry : angle 0.65944 (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 422 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 2.533 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 64 LYS cc_start: 0.6587 (tppt) cc_final: 0.5971 (ttmm) REVERT: A 180 THR cc_start: 0.7822 (p) cc_final: 0.7504 (p) REVERT: A 183 MET cc_start: 0.6502 (mmp) cc_final: 0.5672 (mmp) REVERT: A 312 ILE cc_start: 0.7910 (tt) cc_final: 0.7551 (tt) REVERT: A 343 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 401 MET cc_start: 0.8269 (mmm) cc_final: 0.8012 (mmm) REVERT: B 34 MET cc_start: 0.8587 (mtt) cc_final: 0.8095 (mtt) REVERT: B 38 LYS cc_start: 0.7683 (tptt) cc_final: 0.7350 (tppt) REVERT: B 133 GLU cc_start: 0.8719 (mp0) cc_final: 0.8399 (tm-30) REVERT: B 237 LEU cc_start: 0.9057 (mm) cc_final: 0.8798 (tp) REVERT: B 282 HIS cc_start: 0.7266 (m-70) cc_final: 0.6905 (m170) REVERT: C 42 ASP cc_start: 0.7418 (t0) cc_final: 0.6853 (t0) REVERT: C 137 TYR cc_start: 0.8028 (m-80) cc_final: 0.7580 (m-80) REVERT: C 283 LEU cc_start: 0.8671 (tp) cc_final: 0.8468 (tp) REVERT: C 375 ASP cc_start: 0.8767 (m-30) cc_final: 0.8307 (t0) REVERT: C 394 LYS cc_start: 0.8799 (mptt) cc_final: 0.8425 (tmtt) REVERT: C 448 PHE cc_start: 0.7388 (m-10) cc_final: 0.6976 (m-10) REVERT: D 37 MET cc_start: 0.7507 (tpt) cc_final: 0.7281 (tpt) REVERT: D 41 LEU cc_start: 0.9415 (tp) cc_final: 0.9213 (tp) REVERT: D 49 ILE cc_start: 0.7538 (mm) cc_final: 0.7224 (tp) REVERT: D 52 LYS cc_start: 0.7007 (mmmm) cc_final: 0.5812 (tttt) REVERT: D 136 MET cc_start: 0.3571 (tmm) cc_final: 0.3323 (tmm) REVERT: E 7 ASN cc_start: 0.8892 (t0) cc_final: 0.8677 (t0) REVERT: E 37 MET cc_start: 0.8020 (mmp) cc_final: 0.6755 (mtp) REVERT: E 56 LEU cc_start: 0.8350 (mm) cc_final: 0.7587 (tt) REVERT: E 122 ARG cc_start: 0.4210 (ttt180) cc_final: 0.2879 (mmt180) REVERT: E 129 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7673 (ttm-80) REVERT: F 37 MET cc_start: 0.7224 (ttp) cc_final: 0.6804 (ttm) REVERT: F 47 ASP cc_start: 0.8335 (m-30) cc_final: 0.8066 (m-30) REVERT: F 63 ASP cc_start: 0.6751 (t0) cc_final: 0.6375 (t0) REVERT: F 133 PHE cc_start: 0.5967 (m-80) cc_final: 0.5735 (m-80) REVERT: F 136 MET cc_start: 0.7128 (ptm) cc_final: 0.6686 (ppp) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5715 time to fit residues: 365.5838 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 : 2.229 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130018 restraints weight = 116888.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136107 restraints weight = 55048.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139980 restraints weight = 32758.716| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 15695 Z= 0.195 Angle : 0.691 28.622 21250 Z= 0.362 Chirality : 0.044 0.329 2418 Planarity : 0.004 0.079 2670 Dihedral : 5.606 30.987 2091 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.42 % Favored : 91.37 % 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: -1.85 (0.18), residues: 1971 helix: 0.77 (0.25), residues: 448 sheet: -1.36 (0.22), residues: 517 loop : -2.13 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 220 HIS 0.007 0.001 HIS A 144 PHE 0.024 0.001 PHE F 155 TYR 0.013 0.002 TYR B 444 ARG 0.024 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 629) hydrogen bonds : angle 5.62860 ( 1704) SS BOND : bond 0.00946 ( 26) SS BOND : angle 3.50543 ( 52) covalent geometry : bond 0.00441 (15669) covalent geometry : angle 0.66972 (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 417 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 2.455 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 180 THR cc_start: 0.7804 (p) cc_final: 0.7476 (p) REVERT: A 183 MET cc_start: 0.6549 (mmp) cc_final: 0.5666 (mmp) REVERT: A 201 MET cc_start: 0.8065 (mtt) cc_final: 0.7835 (mtt) REVERT: A 215 ASP cc_start: 0.8598 (m-30) cc_final: 0.8382 (m-30) REVERT: A 312 ILE cc_start: 0.8007 (tt) cc_final: 0.7586 (tt) REVERT: A 343 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 401 MET cc_start: 0.8234 (mmm) cc_final: 0.7951 (mmm) REVERT: B 34 MET cc_start: 0.8572 (mtt) cc_final: 0.8115 (mtt) REVERT: B 38 LYS cc_start: 0.7876 (tptt) cc_final: 0.7477 (tppt) REVERT: B 133 GLU cc_start: 0.8726 (mp0) cc_final: 0.8419 (tm-30) REVERT: B 237 LEU cc_start: 0.9138 (mm) cc_final: 0.8833 (tp) REVERT: B 282 HIS cc_start: 0.7311 (m-70) cc_final: 0.6937 (m170) REVERT: B 334 LYS cc_start: 0.7654 (tttm) cc_final: 0.7398 (tttm) REVERT: B 380 ILE cc_start: 0.7976 (mm) cc_final: 0.7747 (mm) REVERT: C 42 ASP cc_start: 0.7284 (t0) cc_final: 0.6766 (t0) REVERT: C 137 TYR cc_start: 0.8150 (m-80) cc_final: 0.7710 (m-80) REVERT: C 375 ASP cc_start: 0.8596 (m-30) cc_final: 0.8180 (t0) REVERT: C 394 LYS cc_start: 0.8814 (mptt) cc_final: 0.8464 (tmtt) REVERT: C 448 PHE cc_start: 0.7462 (m-10) cc_final: 0.7038 (m-10) REVERT: D 37 MET cc_start: 0.7526 (tpt) cc_final: 0.7241 (tpt) REVERT: D 52 LYS cc_start: 0.7129 (mmmm) cc_final: 0.5867 (tttp) REVERT: D 136 MET cc_start: 0.3299 (tmm) cc_final: 0.3071 (tmm) REVERT: E 7 ASN cc_start: 0.8960 (t0) cc_final: 0.8737 (t0) REVERT: E 37 MET cc_start: 0.8008 (mmp) cc_final: 0.6883 (mtp) REVERT: E 122 ARG cc_start: 0.4133 (ttt180) cc_final: 0.2890 (mmt180) REVERT: E 129 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7665 (ttm-80) REVERT: F 37 MET cc_start: 0.7112 (ttp) cc_final: 0.6675 (ttm) REVERT: F 47 ASP cc_start: 0.8307 (m-30) cc_final: 0.8044 (m-30) REVERT: F 63 ASP cc_start: 0.6897 (t0) cc_final: 0.6529 (t0) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.6058 time to fit residues: 385.9140 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 : 2.361 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.166405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.132267 restraints weight = 106442.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138281 restraints weight = 48994.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142251 restraints weight = 28566.338| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 15695 Z= 0.160 Angle : 0.675 29.419 21250 Z= 0.352 Chirality : 0.044 0.347 2418 Planarity : 0.005 0.171 2670 Dihedral : 5.497 30.254 2091 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.41 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -1.72 (0.18), residues: 1971 helix: 0.88 (0.24), residues: 448 sheet: -1.25 (0.23), residues: 506 loop : -2.06 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 20 HIS 0.005 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 0.04355 ( 629) hydrogen bonds : angle 5.50870 ( 1704) SS BOND : bond 0.00987 ( 26) SS BOND : angle 3.56186 ( 52) covalent geometry : bond 0.00377 (15669) covalent geometry : angle 0.65225 (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 421 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 2.395 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: 0.5710 (m-70) cc_final: 0.5466 (m-70) REVERT: A 183 MET cc_start: 0.6830 (mmp) cc_final: 0.5999 (mmp) REVERT: A 282 HIS cc_start: 0.8505 (m90) cc_final: 0.7904 (m90) REVERT: A 312 ILE cc_start: 0.7987 (tt) cc_final: 0.7675 (tt) REVERT: A 343 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 401 MET cc_start: 0.8177 (mmm) cc_final: 0.7896 (mmm) REVERT: B 6 ILE cc_start: 0.8806 (mm) cc_final: 0.8374 (mm) REVERT: B 34 MET cc_start: 0.8563 (mtt) cc_final: 0.8062 (mtt) REVERT: B 38 LYS cc_start: 0.7873 (tptt) cc_final: 0.7473 (tppt) REVERT: B 133 GLU cc_start: 0.8732 (mp0) cc_final: 0.8378 (tm-30) REVERT: B 237 LEU cc_start: 0.9021 (mm) cc_final: 0.8781 (tp) REVERT: B 303 THR cc_start: 0.8058 (p) cc_final: 0.7729 (t) REVERT: B 380 ILE cc_start: 0.8015 (mm) cc_final: 0.7719 (mm) REVERT: C 42 ASP cc_start: 0.7329 (t0) cc_final: 0.6750 (t0) REVERT: C 137 TYR cc_start: 0.8060 (m-80) cc_final: 0.7617 (m-80) REVERT: C 283 LEU cc_start: 0.8622 (tp) cc_final: 0.8387 (tp) REVERT: C 375 ASP cc_start: 0.8697 (m-30) cc_final: 0.8280 (t0) REVERT: C 394 LYS cc_start: 0.8813 (mptt) cc_final: 0.8456 (tmtt) REVERT: C 448 PHE cc_start: 0.7435 (m-10) cc_final: 0.7010 (m-10) REVERT: D 37 MET cc_start: 0.7409 (tpt) cc_final: 0.7207 (tpt) REVERT: D 41 LEU cc_start: 0.9418 (tp) cc_final: 0.9195 (tp) REVERT: D 52 LYS cc_start: 0.6949 (mmmm) cc_final: 0.5710 (tttp) REVERT: D 136 MET cc_start: 0.3437 (tmm) cc_final: 0.3202 (tmm) REVERT: E 7 ASN cc_start: 0.8964 (t0) cc_final: 0.8726 (t0) REVERT: E 37 MET cc_start: 0.8086 (mmp) cc_final: 0.6782 (mtp) REVERT: E 56 LEU cc_start: 0.8331 (mm) cc_final: 0.7456 (tt) REVERT: E 129 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7677 (ttm-80) REVERT: F 37 MET cc_start: 0.7257 (ttp) cc_final: 0.6699 (ttm) REVERT: F 47 ASP cc_start: 0.8336 (m-30) cc_final: 0.8082 (m-30) REVERT: F 63 ASP cc_start: 0.6922 (t0) cc_final: 0.6557 (t0) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.5367 time to fit residues: 343.3801 Evaluate side-chains 367 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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: 4.9990 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 158 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.167400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132481 restraints weight = 110193.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138733 restraints weight = 51060.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142798 restraints weight = 29786.385| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.163 15695 Z= 0.143 Angle : 0.669 30.340 21250 Z= 0.347 Chirality : 0.044 0.344 2418 Planarity : 0.004 0.118 2670 Dihedral : 5.359 31.448 2091 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.49 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.59 (0.19), residues: 1971 helix: 0.97 (0.24), residues: 449 sheet: -1.20 (0.22), residues: 511 loop : -1.96 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 391 HIS 0.010 0.001 HIS C 282 PHE 0.025 0.001 PHE F 155 TYR 0.010 0.001 TYR C 444 ARG 0.008 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 629) hydrogen bonds : angle 5.38141 ( 1704) SS BOND : bond 0.00968 ( 26) SS BOND : angle 3.79032 ( 52) covalent geometry : bond 0.00347 (15669) covalent geometry : angle 0.64312 (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 425 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.5670 (m-70) cc_final: 0.5241 (m-70) REVERT: A 183 MET cc_start: 0.6809 (mmp) cc_final: 0.5968 (mmp) REVERT: A 282 HIS cc_start: 0.8484 (m90) cc_final: 0.7857 (m90) REVERT: A 343 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 392 PHE cc_start: 0.8400 (t80) cc_final: 0.7979 (t80) REVERT: A 401 MET cc_start: 0.8114 (mmm) cc_final: 0.7823 (mmm) REVERT: B 38 LYS cc_start: 0.8069 (tptt) cc_final: 0.7656 (tppt) REVERT: B 125 MET cc_start: 0.7558 (mmm) cc_final: 0.6518 (mmt) REVERT: B 133 GLU cc_start: 0.8705 (mp0) cc_final: 0.8366 (tm-30) REVERT: B 237 LEU cc_start: 0.9091 (mm) cc_final: 0.8708 (tp) REVERT: B 260 MET cc_start: 0.8394 (mmp) cc_final: 0.8009 (mmm) REVERT: B 303 THR cc_start: 0.8074 (p) cc_final: 0.7752 (t) REVERT: B 334 LYS cc_start: 0.7591 (tttm) cc_final: 0.7363 (tttm) REVERT: B 380 ILE cc_start: 0.7821 (mm) cc_final: 0.7563 (mm) REVERT: C 42 ASP cc_start: 0.7311 (t0) cc_final: 0.6720 (t0) REVERT: C 137 TYR cc_start: 0.8017 (m-80) cc_final: 0.7587 (m-80) REVERT: C 375 ASP cc_start: 0.8675 (m-30) cc_final: 0.8260 (t0) REVERT: C 394 LYS cc_start: 0.8803 (mptt) cc_final: 0.8440 (tmtt) REVERT: C 448 PHE cc_start: 0.7411 (m-10) cc_final: 0.6988 (m-10) REVERT: D 41 LEU cc_start: 0.9415 (tp) cc_final: 0.9190 (tp) REVERT: D 52 LYS cc_start: 0.6836 (mmmm) cc_final: 0.5545 (tttp) REVERT: D 136 MET cc_start: 0.3355 (tmm) cc_final: 0.3128 (tmm) REVERT: E 7 ASN cc_start: 0.8951 (t0) cc_final: 0.8716 (t0) REVERT: E 37 MET cc_start: 0.7997 (mmp) cc_final: 0.6694 (mtp) REVERT: E 56 LEU cc_start: 0.8442 (mm) cc_final: 0.7555 (tt) REVERT: E 129 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7652 (ttm-80) REVERT: F 47 ASP cc_start: 0.8282 (m-30) cc_final: 0.8046 (m-30) REVERT: F 63 ASP cc_start: 0.6895 (t0) cc_final: 0.6524 (t0) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.5597 time to fit residues: 362.3793 Evaluate side-chains 374 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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: 0.4980 chunk 105 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 437 HIS ** F 59 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.165824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131501 restraints weight = 105383.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137543 restraints weight = 48663.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141505 restraints weight = 28386.451| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 15695 Z= 0.158 Angle : 0.676 31.597 21250 Z= 0.351 Chirality : 0.044 0.351 2418 Planarity : 0.004 0.106 2670 Dihedral : 5.304 30.250 2091 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.53 (0.19), residues: 1971 helix: 1.07 (0.24), residues: 450 sheet: -1.13 (0.22), residues: 522 loop : -1.97 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 20 HIS 0.009 0.001 HIS B 437 PHE 0.024 0.001 PHE F 155 TYR 0.010 0.001 TYR A 326 ARG 0.010 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 629) hydrogen bonds : angle 5.33171 ( 1704) SS BOND : bond 0.00751 ( 26) SS BOND : angle 3.72470 ( 52) covalent geometry : bond 0.00382 (15669) covalent geometry : angle 0.65168 (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 422 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.5650 (m-70) cc_final: 0.5411 (m-70) REVERT: A 183 MET cc_start: 0.6673 (mmp) cc_final: 0.5769 (mmp) REVERT: A 282 HIS cc_start: 0.8425 (m90) cc_final: 0.7834 (m90) REVERT: A 343 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 401 MET cc_start: 0.8235 (mmm) cc_final: 0.7966 (mmm) REVERT: B 38 LYS cc_start: 0.8143 (tptt) cc_final: 0.7730 (tppt) REVERT: B 133 GLU cc_start: 0.8614 (mp0) cc_final: 0.8293 (tm-30) REVERT: B 211 GLN cc_start: 0.9166 (pm20) cc_final: 0.8945 (pm20) REVERT: B 237 LEU cc_start: 0.9134 (mm) cc_final: 0.8800 (tp) REVERT: B 303 THR cc_start: 0.7888 (p) cc_final: 0.7640 (t) REVERT: B 334 LYS cc_start: 0.7553 (tttm) cc_final: 0.7341 (tttm) REVERT: B 380 ILE cc_start: 0.8200 (mm) cc_final: 0.7874 (mm) REVERT: C 42 ASP cc_start: 0.7228 (t0) cc_final: 0.6686 (t0) REVERT: C 137 TYR cc_start: 0.8113 (m-80) cc_final: 0.7706 (m-80) REVERT: C 283 LEU cc_start: 0.8688 (tp) cc_final: 0.8437 (tp) REVERT: C 375 ASP cc_start: 0.8568 (m-30) cc_final: 0.8214 (t0) REVERT: C 394 LYS cc_start: 0.8779 (mptt) cc_final: 0.8445 (tmtt) REVERT: C 448 PHE cc_start: 0.7392 (m-10) cc_final: 0.6960 (m-10) REVERT: D 41 LEU cc_start: 0.9372 (tp) cc_final: 0.9159 (tp) REVERT: D 52 LYS cc_start: 0.6943 (mmmm) cc_final: 0.5629 (tttt) REVERT: D 136 MET cc_start: 0.3467 (tmm) cc_final: 0.3202 (tmm) REVERT: E 7 ASN cc_start: 0.8928 (t0) cc_final: 0.8704 (t0) REVERT: E 37 MET cc_start: 0.7972 (mmp) cc_final: 0.6722 (mtp) REVERT: E 56 LEU cc_start: 0.8495 (mm) cc_final: 0.7637 (tt) REVERT: E 129 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7692 (ttm-80) REVERT: F 63 ASP cc_start: 0.6974 (t0) cc_final: 0.6613 (t0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5340 time to fit residues: 342.3525 Evaluate side-chains 370 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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: 9.9990 chunk 52 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** 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 = 0.4204 r_free = 0.4204 target = 0.166058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132006 restraints weight = 105545.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138041 restraints weight = 48519.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142014 restraints weight = 28210.876| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 15695 Z= 0.157 Angle : 0.675 32.235 21250 Z= 0.349 Chirality : 0.044 0.374 2418 Planarity : 0.004 0.102 2670 Dihedral : 5.296 29.619 2091 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.05 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.54 (0.19), residues: 1971 helix: 1.02 (0.24), residues: 450 sheet: -1.14 (0.23), residues: 518 loop : -1.96 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 20 HIS 0.008 0.001 HIS E 86 PHE 0.029 0.001 PHE C 306 TYR 0.012 0.001 TYR C 299 ARG 0.011 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 629) hydrogen bonds : angle 5.30829 ( 1704) SS BOND : bond 0.01148 ( 26) SS BOND : angle 3.84458 ( 52) covalent geometry : bond 0.00378 (15669) covalent geometry : angle 0.64859 (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 424 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.5676 (m-70) cc_final: 0.5429 (m-70) REVERT: A 183 MET cc_start: 0.6793 (mmp) cc_final: 0.5879 (mmp) REVERT: A 282 HIS cc_start: 0.8458 (m90) cc_final: 0.7857 (m90) REVERT: A 343 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 373 PHE cc_start: 0.7966 (m-80) cc_final: 0.7690 (m-80) REVERT: A 401 MET cc_start: 0.8186 (mmm) cc_final: 0.7903 (mmm) REVERT: B 38 LYS cc_start: 0.8144 (tptt) cc_final: 0.7720 (tppt) REVERT: B 125 MET cc_start: 0.7644 (mmm) cc_final: 0.6717 (mmt) REVERT: B 133 GLU cc_start: 0.8656 (mp0) cc_final: 0.8306 (tm-30) REVERT: B 237 LEU cc_start: 0.9112 (mm) cc_final: 0.8762 (tp) REVERT: B 260 MET cc_start: 0.8477 (mmp) cc_final: 0.8082 (mmm) REVERT: B 303 THR cc_start: 0.7974 (p) cc_final: 0.7734 (t) REVERT: B 380 ILE cc_start: 0.7997 (mm) cc_final: 0.7732 (mm) REVERT: B 386 GLN cc_start: 0.8175 (pt0) cc_final: 0.7809 (pp30) REVERT: C 42 ASP cc_start: 0.7294 (t0) cc_final: 0.6704 (t0) REVERT: C 137 TYR cc_start: 0.8112 (m-80) cc_final: 0.7684 (m-80) REVERT: C 283 LEU cc_start: 0.8656 (tp) cc_final: 0.8424 (tp) REVERT: C 375 ASP cc_start: 0.8681 (m-30) cc_final: 0.8292 (t0) REVERT: C 394 LYS cc_start: 0.8816 (mptt) cc_final: 0.8460 (tmtt) REVERT: C 448 PHE cc_start: 0.7426 (m-10) cc_final: 0.6874 (m-10) REVERT: D 41 LEU cc_start: 0.9418 (tp) cc_final: 0.9191 (tp) REVERT: D 52 LYS cc_start: 0.6900 (mmmm) cc_final: 0.5606 (tttt) REVERT: D 136 MET cc_start: 0.3545 (tmm) cc_final: 0.3292 (tmm) REVERT: E 7 ASN cc_start: 0.8971 (t0) cc_final: 0.8743 (t0) REVERT: E 37 MET cc_start: 0.8005 (mmp) cc_final: 0.6676 (mtp) REVERT: E 56 LEU cc_start: 0.8456 (mm) cc_final: 0.7629 (tt) REVERT: E 129 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7683 (ttm-80) REVERT: F 47 ASP cc_start: 0.8248 (m-30) cc_final: 0.8041 (m-30) REVERT: F 63 ASP cc_start: 0.6997 (t0) cc_final: 0.6633 (t0) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.5602 time to fit residues: 360.3047 Evaluate side-chains 371 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 152 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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** ** 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 = 0.4201 r_free = 0.4201 target = 0.165827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131489 restraints weight = 104557.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137520 restraints weight = 48130.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141467 restraints weight = 28027.929| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 15695 Z= 0.158 Angle : 0.678 30.893 21250 Z= 0.351 Chirality : 0.044 0.346 2418 Planarity : 0.005 0.159 2670 Dihedral : 5.300 29.419 2091 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.26 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 1.00 (0.25), residues: 444 sheet: -1.10 (0.23), residues: 518 loop : -1.98 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 20 HIS 0.004 0.001 HIS B 437 PHE 0.039 0.001 PHE C 306 TYR 0.039 0.002 TYR D 142 ARG 0.005 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 629) hydrogen bonds : angle 5.29615 ( 1704) SS BOND : bond 0.01046 ( 26) SS BOND : angle 3.81789 ( 52) covalent geometry : bond 0.00381 (15669) covalent geometry : angle 0.65147 (21198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11305.27 seconds wall clock time: 193 minutes 38.50 seconds (11618.50 seconds total)