Starting phenix.real_space_refine on Tue Jul 29 08:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.map" model { file = "/net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pxw_20523/07_2025/6pxw_20523.cif" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 7116 2.51 5 N 1912 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "B" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "F" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 6.96, per 1000 atoms: 0.62 Number of scatterers: 11198 At special positions: 0 Unit cell: (129.47, 129.47, 87.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2064 8.00 N 1912 7.00 C 7116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.02 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.04 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 22 sheets defined 21.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.849A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.666A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.059A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.904A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.850A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.665A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.060A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 692 through 714 removed outlier: 3.611A pdb=" N SER B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 67 through 73 removed outlier: 3.640A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.864A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.388A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE A 534 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 64 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.863A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC1, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.389A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC3, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE B 534 " --> pdb=" O PHE B 503 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 600 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: 3.71 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3533 1.34 - 1.46: 2575 1.46 - 1.58: 5226 1.58 - 1.70: 0 1.70 - 1.83: 124 Bond restraints: 11458 Sorted by residual: bond pdb=" C ILE B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" C ILE A 285 " pdb=" N PRO A 286 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.30e-02 5.92e+03 4.63e+00 bond pdb=" CG1 ILE A 95 " pdb=" CD1 ILE A 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CB VAL B 179 " pdb=" CG2 VAL B 179 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 ... (remaining 11453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 14894 2.25 - 4.50: 532 4.50 - 6.74: 69 6.74 - 8.99: 12 8.99 - 11.24: 3 Bond angle restraints: 15510 Sorted by residual: angle pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N HIS F 10 " pdb=" CA HIS F 10 " pdb=" C HIS F 10 " ideal model delta sigma weight residual 111.07 104.96 6.11 1.07e+00 8.73e-01 3.26e+01 angle pdb=" N HIS E 10 " pdb=" CA HIS E 10 " pdb=" C HIS E 10 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 15505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.02: 6224 12.02 - 24.04: 550 24.04 - 36.06: 101 36.06 - 48.08: 43 48.08 - 60.10: 26 Dihedral angle restraints: 6944 sinusoidal: 2902 harmonic: 4042 Sorted by residual: dihedral pdb=" CA THR B 578 " pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta harmonic sigma weight residual 180.00 137.11 42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1186 0.056 - 0.112: 383 0.112 - 0.168: 106 0.168 - 0.224: 9 0.224 - 0.279: 8 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1689 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C THR B 578 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 578 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR B 579 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 542 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 543 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 542 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO B 543 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.036 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2474 2.78 - 3.31: 9097 3.31 - 3.84: 17401 3.84 - 4.37: 20428 4.37 - 4.90: 36084 Nonbonded interactions: 85484 Sorted by model distance: nonbonded pdb=" OE2 GLU A 698 " pdb=" OH TYR B 144 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 698 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU B 355 " pdb=" NH2 ARG B 383 " model vdw 2.334 3.120 ... (remaining 85479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) selection = chain 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.008 0.074 11498 Z= 0.360 Angle : 0.996 11.238 15590 Z= 0.556 Chirality : 0.060 0.279 1692 Planarity : 0.007 0.066 1994 Dihedral : 9.829 58.761 4216 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.85 % Favored : 89.63 % Rotamer: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.04 (0.18), residues: 1350 helix: -3.24 (0.25), residues: 224 sheet: -2.94 (0.28), residues: 174 loop : -2.66 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 414 HIS 0.015 0.003 HIS B 280 PHE 0.025 0.004 PHE A 565 TYR 0.032 0.003 TYR B 579 ARG 0.008 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.21433 ( 228) hydrogen bonds : angle 8.56370 ( 600) SS BOND : bond 0.00539 ( 40) SS BOND : angle 1.54152 ( 80) covalent geometry : bond 0.00846 (11458) covalent geometry : angle 0.99239 (15510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6893 (mtm-85) REVERT: B 42 ARG cc_start: 0.7404 (mmm160) cc_final: 0.6920 (mtm-85) REVERT: D 15 LEU cc_start: 0.8572 (mt) cc_final: 0.8365 (mt) REVERT: F 70 GLN cc_start: 0.8138 (mp-120) cc_final: 0.7832 (mt0) outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.3374 time to fit residues: 93.9962 Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.0030 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 32 HIS A 100 HIS A 175 ASN A 209 HIS A 247 HIS A 328 GLN A 357 ASN A 405 ASN A 407 ASN A 546 GLN A 561 GLN B 15 ASN B 32 HIS B 100 HIS B 175 ASN B 209 HIS B 247 HIS B 328 GLN B 405 ASN B 407 ASN B 546 GLN B 561 GLN D 70 GLN F 70 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094013 restraints weight = 18679.480| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.78 r_work: 0.3179 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11498 Z= 0.121 Angle : 0.609 9.202 15590 Z= 0.323 Chirality : 0.045 0.176 1692 Planarity : 0.004 0.052 1994 Dihedral : 6.003 32.610 1508 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 0.63 % Allowed : 6.23 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.36 (0.20), residues: 1350 helix: -2.00 (0.29), residues: 252 sheet: -2.17 (0.36), residues: 140 loop : -2.47 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.004 0.001 HIS B 440 PHE 0.013 0.001 PHE B 565 TYR 0.013 0.001 TYR E 74 ARG 0.008 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 228) hydrogen bonds : angle 6.34306 ( 600) SS BOND : bond 0.00299 ( 40) SS BOND : angle 1.41119 ( 80) covalent geometry : bond 0.00263 (11458) covalent geometry : angle 0.60170 (15510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6754 (mtm-85) REVERT: A 47 ARG cc_start: 0.7228 (mtm110) cc_final: 0.6880 (mmp-170) REVERT: A 135 ARG cc_start: 0.8143 (mmt180) cc_final: 0.7915 (mmt180) REVERT: A 138 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 589 GLN cc_start: 0.7711 (pt0) cc_final: 0.7483 (tt0) REVERT: B 42 ARG cc_start: 0.7584 (mmm160) cc_final: 0.6729 (mtm-85) REVERT: B 47 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6923 (mmp-170) REVERT: B 138 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8215 (t0) REVERT: B 371 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7989 (ttp80) REVERT: B 589 GLN cc_start: 0.7639 (pt0) cc_final: 0.7399 (tt0) REVERT: C 72 GLU cc_start: 0.8123 (tp30) cc_final: 0.7864 (tp30) REVERT: F 60 GLN cc_start: 0.5612 (mt0) cc_final: 0.5054 (pt0) REVERT: F 70 GLN cc_start: 0.8298 (mp10) cc_final: 0.7681 (mt0) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.2793 time to fit residues: 46.5002 Evaluate side-chains 96 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 290 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 0.0570 chunk 42 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 295 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092905 restraints weight = 18879.794| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.79 r_work: 0.3169 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11498 Z= 0.122 Angle : 0.561 7.318 15590 Z= 0.298 Chirality : 0.044 0.136 1692 Planarity : 0.004 0.049 1994 Dihedral : 5.516 35.199 1508 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 0.95 % Allowed : 7.49 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.86 (0.21), residues: 1350 helix: -1.34 (0.31), residues: 252 sheet: -1.82 (0.38), residues: 140 loop : -2.22 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.004 0.001 HIS B 710 PHE 0.011 0.001 PHE B 565 TYR 0.015 0.001 TYR E 74 ARG 0.004 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 228) hydrogen bonds : angle 5.93173 ( 600) SS BOND : bond 0.00291 ( 40) SS BOND : angle 0.88879 ( 80) covalent geometry : bond 0.00284 (11458) covalent geometry : angle 0.55924 (15510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7579 (mmm160) cc_final: 0.6792 (mtm-85) REVERT: A 47 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6879 (mmp-170) REVERT: A 546 GLN cc_start: 0.7492 (tp40) cc_final: 0.7284 (tp-100) REVERT: A 589 GLN cc_start: 0.7659 (pt0) cc_final: 0.7453 (tt0) REVERT: B 42 ARG cc_start: 0.7575 (mmm160) cc_final: 0.6769 (mtm-85) REVERT: B 47 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6879 (mmp-170) REVERT: B 135 ARG cc_start: 0.8132 (mmt180) cc_final: 0.7885 (mmm160) REVERT: B 138 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8205 (t0) REVERT: B 371 ARG cc_start: 0.8260 (ttp-170) cc_final: 0.7978 (ttp80) REVERT: B 546 GLN cc_start: 0.7595 (tp40) cc_final: 0.7328 (tp-100) REVERT: B 589 GLN cc_start: 0.7669 (pt0) cc_final: 0.7459 (tt0) REVERT: F 60 GLN cc_start: 0.5656 (mt0) cc_final: 0.5250 (pt0) REVERT: F 70 GLN cc_start: 0.8357 (mp10) cc_final: 0.7886 (mt0) outliers start: 12 outliers final: 4 residues processed: 108 average time/residue: 0.2550 time to fit residues: 39.0249 Evaluate side-chains 87 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 429 HIS A 513 GLN A 561 GLN B 280 HIS B 295 ASN B 429 HIS B 513 GLN B 561 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086908 restraints weight = 18840.587| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.71 r_work: 0.3069 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 11498 Z= 0.314 Angle : 0.742 7.175 15590 Z= 0.384 Chirality : 0.050 0.165 1692 Planarity : 0.005 0.046 1994 Dihedral : 6.076 46.650 1508 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.30 % Favored : 89.63 % Rotamer: Outliers : 1.66 % Allowed : 7.97 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.97 (0.21), residues: 1350 helix: -1.41 (0.31), residues: 248 sheet: -2.26 (0.34), residues: 174 loop : -2.21 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 412 HIS 0.008 0.002 HIS A 548 PHE 0.018 0.002 PHE B 506 TYR 0.025 0.002 TYR B 401 ARG 0.005 0.001 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 228) hydrogen bonds : angle 6.22064 ( 600) SS BOND : bond 0.00477 ( 40) SS BOND : angle 1.41626 ( 80) covalent geometry : bond 0.00759 (11458) covalent geometry : angle 0.73644 (15510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7620 (mmm160) cc_final: 0.6814 (mtm-85) REVERT: A 47 ARG cc_start: 0.7221 (mtm110) cc_final: 0.6729 (mmp-170) REVERT: A 218 GLN cc_start: 0.7416 (mt0) cc_final: 0.6828 (tt0) REVERT: A 546 GLN cc_start: 0.7817 (tp40) cc_final: 0.7479 (tp-100) REVERT: B 42 ARG cc_start: 0.7620 (mmm160) cc_final: 0.6810 (mtm-85) REVERT: B 47 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6740 (mmp-170) REVERT: B 138 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 218 GLN cc_start: 0.7424 (mt0) cc_final: 0.6880 (tt0) REVERT: B 371 ARG cc_start: 0.8459 (ttp-170) cc_final: 0.8174 (ttp80) REVERT: B 546 GLN cc_start: 0.7868 (tp40) cc_final: 0.7498 (tp-100) outliers start: 21 outliers final: 7 residues processed: 107 average time/residue: 0.3957 time to fit residues: 57.7248 Evaluate side-chains 89 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 130 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 452 GLN B 328 GLN B 452 GLN D 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089589 restraints weight = 18773.226| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.87 r_work: 0.3089 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11498 Z= 0.146 Angle : 0.580 7.287 15590 Z= 0.307 Chirality : 0.044 0.137 1692 Planarity : 0.004 0.046 1994 Dihedral : 5.611 39.467 1508 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 0.87 % Allowed : 9.07 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.69 (0.22), residues: 1350 helix: -1.12 (0.32), residues: 248 sheet: -1.94 (0.39), residues: 140 loop : -2.09 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.004 0.001 HIS A 548 PHE 0.011 0.001 PHE A 565 TYR 0.013 0.001 TYR B 401 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 228) hydrogen bonds : angle 5.88172 ( 600) SS BOND : bond 0.00285 ( 40) SS BOND : angle 0.98300 ( 80) covalent geometry : bond 0.00350 (11458) covalent geometry : angle 0.57734 (15510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7543 (mmm160) cc_final: 0.6825 (mtm-85) REVERT: A 47 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6647 (mmp-170) REVERT: A 218 GLN cc_start: 0.7439 (mt0) cc_final: 0.6816 (tt0) REVERT: A 546 GLN cc_start: 0.7707 (tp40) cc_final: 0.7324 (tp-100) REVERT: A 554 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7386 (pmm150) REVERT: B 42 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6804 (mtm-85) REVERT: B 47 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6653 (mmp-170) REVERT: B 138 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8110 (t0) REVERT: B 218 GLN cc_start: 0.7401 (mt0) cc_final: 0.6809 (tt0) REVERT: B 371 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8048 (ttp80) REVERT: B 546 GLN cc_start: 0.7697 (tp40) cc_final: 0.7301 (tp-100) REVERT: B 554 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7680 (pmm150) outliers start: 11 outliers final: 3 residues processed: 96 average time/residue: 0.2974 time to fit residues: 39.5083 Evaluate side-chains 86 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 554 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090925 restraints weight = 18935.970| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.71 r_work: 0.3134 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11498 Z= 0.115 Angle : 0.534 7.123 15590 Z= 0.283 Chirality : 0.043 0.136 1692 Planarity : 0.004 0.045 1994 Dihedral : 5.224 33.838 1508 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.78 % Rotamer: Outliers : 1.26 % Allowed : 9.62 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.51 (0.22), residues: 1350 helix: -0.89 (0.32), residues: 248 sheet: -1.88 (0.40), residues: 140 loop : -1.97 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.015 0.001 HIS B 185 PHE 0.011 0.001 PHE B 565 TYR 0.012 0.001 TYR A 507 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 228) hydrogen bonds : angle 5.70186 ( 600) SS BOND : bond 0.00252 ( 40) SS BOND : angle 0.82477 ( 80) covalent geometry : bond 0.00275 (11458) covalent geometry : angle 0.53178 (15510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7603 (mmm160) cc_final: 0.6875 (mtm-85) REVERT: A 47 ARG cc_start: 0.7066 (mtm110) cc_final: 0.6623 (mmp-170) REVERT: A 218 GLN cc_start: 0.7432 (mt0) cc_final: 0.6817 (tt0) REVERT: A 546 GLN cc_start: 0.7650 (tp40) cc_final: 0.7327 (tp-100) REVERT: A 554 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7330 (pmm150) REVERT: B 42 ARG cc_start: 0.7622 (mmm160) cc_final: 0.6899 (mtm-85) REVERT: B 47 ARG cc_start: 0.7085 (mtm110) cc_final: 0.6624 (mmp-170) REVERT: B 138 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7948 (t0) REVERT: B 218 GLN cc_start: 0.7418 (mt0) cc_final: 0.6833 (tt0) REVERT: B 371 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.8028 (ttp80) REVERT: B 546 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7380 (tp-100) REVERT: B 554 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7558 (pmm150) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 0.2639 time to fit residues: 39.2600 Evaluate side-chains 91 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 110 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091440 restraints weight = 19060.976| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.57 r_work: 0.3097 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11498 Z= 0.155 Angle : 0.560 7.269 15590 Z= 0.295 Chirality : 0.044 0.140 1692 Planarity : 0.004 0.043 1994 Dihedral : 5.250 35.136 1508 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.52 % Favored : 91.41 % Rotamer: Outliers : 1.50 % Allowed : 10.09 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.48 (0.22), residues: 1350 helix: -0.83 (0.33), residues: 248 sheet: -2.00 (0.39), residues: 140 loop : -1.94 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.004 0.001 HIS B 548 PHE 0.011 0.001 PHE B 565 TYR 0.014 0.001 TYR B 579 ARG 0.002 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 228) hydrogen bonds : angle 5.74505 ( 600) SS BOND : bond 0.00269 ( 40) SS BOND : angle 0.89907 ( 80) covalent geometry : bond 0.00373 (11458) covalent geometry : angle 0.55811 (15510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7644 (mmm160) cc_final: 0.6910 (mtm-85) REVERT: A 47 ARG cc_start: 0.7078 (mtm110) cc_final: 0.6616 (mmp-170) REVERT: A 218 GLN cc_start: 0.7445 (mt0) cc_final: 0.6932 (mp10) REVERT: A 546 GLN cc_start: 0.7764 (tp40) cc_final: 0.7463 (tp-100) REVERT: A 554 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7616 (pmm150) REVERT: B 42 ARG cc_start: 0.7629 (mmm160) cc_final: 0.6911 (mtm-85) REVERT: B 47 ARG cc_start: 0.7093 (mtm110) cc_final: 0.6612 (mmp-170) REVERT: B 138 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7941 (t0) REVERT: B 218 GLN cc_start: 0.7460 (mt0) cc_final: 0.6847 (tt0) REVERT: B 262 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 371 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.8091 (ttp80) REVERT: B 546 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7498 (tp-100) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.3493 time to fit residues: 50.2711 Evaluate side-chains 97 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.118573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091639 restraints weight = 18892.748| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.78 r_work: 0.3109 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11498 Z= 0.115 Angle : 0.527 7.525 15590 Z= 0.279 Chirality : 0.043 0.137 1692 Planarity : 0.003 0.042 1994 Dihedral : 5.059 32.366 1508 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.42 % Allowed : 10.41 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.34 (0.22), residues: 1350 helix: -0.66 (0.33), residues: 248 sheet: -2.04 (0.41), residues: 130 loop : -1.85 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.003 0.001 HIS A 548 PHE 0.011 0.001 PHE B 565 TYR 0.013 0.001 TYR B 579 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 228) hydrogen bonds : angle 5.65494 ( 600) SS BOND : bond 0.00224 ( 40) SS BOND : angle 0.79356 ( 80) covalent geometry : bond 0.00274 (11458) covalent geometry : angle 0.52561 (15510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7607 (mmm160) cc_final: 0.6870 (mtm-85) REVERT: A 47 ARG cc_start: 0.7055 (mtm110) cc_final: 0.6578 (mmp-170) REVERT: A 218 GLN cc_start: 0.7433 (mt0) cc_final: 0.6902 (mp10) REVERT: A 546 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7415 (tp-100) REVERT: A 554 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7473 (pmm150) REVERT: B 42 ARG cc_start: 0.7578 (mmm160) cc_final: 0.6842 (mtm-85) REVERT: B 47 ARG cc_start: 0.7073 (mtm110) cc_final: 0.6575 (mmp-170) REVERT: B 138 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7993 (t0) REVERT: B 218 GLN cc_start: 0.7443 (mt0) cc_final: 0.6913 (mp10) REVERT: B 371 ARG cc_start: 0.8305 (ttp-170) cc_final: 0.8037 (ttp80) REVERT: B 546 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7409 (tp-100) REVERT: B 554 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7160 (pmm150) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 0.3374 time to fit residues: 48.1191 Evaluate side-chains 93 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.117581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090167 restraints weight = 18885.173| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.70 r_work: 0.3118 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11498 Z= 0.149 Angle : 0.551 7.635 15590 Z= 0.290 Chirality : 0.044 0.137 1692 Planarity : 0.004 0.042 1994 Dihedral : 5.101 34.095 1508 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.50 % Allowed : 10.41 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.33 (0.22), residues: 1350 helix: -0.61 (0.33), residues: 248 sheet: -2.08 (0.41), residues: 130 loop : -1.84 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.004 0.001 HIS B 548 PHE 0.011 0.001 PHE A 565 TYR 0.014 0.001 TYR B 579 ARG 0.002 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 228) hydrogen bonds : angle 5.69167 ( 600) SS BOND : bond 0.00254 ( 40) SS BOND : angle 0.85480 ( 80) covalent geometry : bond 0.00361 (11458) covalent geometry : angle 0.54861 (15510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7618 (mmm160) cc_final: 0.6913 (mtm-85) REVERT: A 47 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6573 (mmp-170) REVERT: A 218 GLN cc_start: 0.7435 (mt0) cc_final: 0.6920 (mp10) REVERT: A 546 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7570 (tp-100) REVERT: A 554 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7615 (pmm150) REVERT: B 42 ARG cc_start: 0.7611 (mmm160) cc_final: 0.6916 (mtm-85) REVERT: B 138 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7957 (t0) REVERT: B 218 GLN cc_start: 0.7457 (mt0) cc_final: 0.6938 (mp10) REVERT: B 265 LYS cc_start: 0.8472 (mtmt) cc_final: 0.7831 (ttpp) REVERT: B 370 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 371 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.8037 (ttp80) REVERT: B 546 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7470 (tp-100) REVERT: B 554 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7278 (pmm150) outliers start: 19 outliers final: 10 residues processed: 97 average time/residue: 0.3688 time to fit residues: 52.6152 Evaluate side-chains 97 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 0.0370 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092033 restraints weight = 18936.708| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.74 r_work: 0.3136 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11498 Z= 0.098 Angle : 0.519 7.593 15590 Z= 0.275 Chirality : 0.043 0.135 1692 Planarity : 0.003 0.045 1994 Dihedral : 4.959 32.285 1508 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.03 % Allowed : 10.88 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.21 (0.22), residues: 1350 helix: -0.49 (0.33), residues: 248 sheet: -1.98 (0.42), residues: 130 loop : -1.77 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.004 0.001 HIS A 548 PHE 0.011 0.001 PHE B 565 TYR 0.012 0.001 TYR B 579 ARG 0.012 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 228) hydrogen bonds : angle 5.62554 ( 600) SS BOND : bond 0.00196 ( 40) SS BOND : angle 0.75225 ( 80) covalent geometry : bond 0.00228 (11458) covalent geometry : angle 0.51801 (15510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7577 (mmm160) cc_final: 0.6871 (mtm-85) REVERT: A 47 ARG cc_start: 0.7005 (mtm110) cc_final: 0.6541 (mmp-170) REVERT: A 218 GLN cc_start: 0.7408 (mt0) cc_final: 0.6887 (mp10) REVERT: A 265 LYS cc_start: 0.8456 (mtmt) cc_final: 0.7866 (ttpp) REVERT: A 546 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7512 (tp-100) REVERT: A 554 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7369 (pmm150) REVERT: B 42 ARG cc_start: 0.7561 (mmm160) cc_final: 0.6851 (mtm-85) REVERT: B 138 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 218 GLN cc_start: 0.7420 (mt0) cc_final: 0.6898 (mp10) REVERT: B 265 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7816 (ttpp) REVERT: B 371 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7984 (ttp80) REVERT: B 546 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7438 (tp-100) REVERT: B 554 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7103 (pmm150) outliers start: 13 outliers final: 6 residues processed: 94 average time/residue: 0.2811 time to fit residues: 37.4045 Evaluate side-chains 93 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090738 restraints weight = 18685.939| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.69 r_work: 0.3125 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11498 Z= 0.134 Angle : 0.539 7.752 15590 Z= 0.283 Chirality : 0.044 0.134 1692 Planarity : 0.003 0.041 1994 Dihedral : 4.978 33.912 1508 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.18 % Allowed : 11.04 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.20 (0.22), residues: 1350 helix: -0.48 (0.33), residues: 248 sheet: -2.01 (0.42), residues: 130 loop : -1.76 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.004 0.001 HIS B 548 PHE 0.010 0.001 PHE B 565 TYR 0.013 0.001 TYR B 579 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 228) hydrogen bonds : angle 5.67652 ( 600) SS BOND : bond 0.00235 ( 40) SS BOND : angle 0.80489 ( 80) covalent geometry : bond 0.00324 (11458) covalent geometry : angle 0.53725 (15510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5499.73 seconds wall clock time: 100 minutes 23.08 seconds (6023.08 seconds total)