Starting phenix.real_space_refine on Sat Sep 12 23:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zje_14746/09_2026/7zje_14746.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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 112 5.16 5 C 12656 2.51 5 N 3224 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 3.90, per 1000 atoms: 0.20 Number of scatterers: 19284 At special positions: 0 Unit cell: (148.12, 148.12, 115.957, 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 112 16.00 O 3292 8.00 N 3224 7.00 C 12656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.69 Conformation dependent library (CDL) restraints added in 763.3 milliseconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 66.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.605A pdb=" N THR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 414 Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER A 466 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.581A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 537 removed outlier: 4.283A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.766A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 414 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER B 466 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.583A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.711A pdb=" N GLN C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.548A pdb=" N MET C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 414 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER C 466 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE D 81 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 414 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER D 466 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 332 1036 hydrogen bonds defined for protein. 2976 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: 3.02 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5996 1.35 - 1.46: 4844 1.46 - 1.58: 8748 1.58 - 1.70: 0 1.70 - 1.81: 172 Bond restraints: 19760 Sorted by residual: bond pdb=" N MET A 640 " pdb=" CA MET A 640 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" N MET D 640 " pdb=" CA MET D 640 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.59e+00 bond pdb=" N MET C 640 " pdb=" CA MET C 640 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.03e+00 bond pdb=" N MET B 640 " pdb=" CA MET B 640 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.89e+00 bond pdb=" C GLU A 376 " pdb=" N PRO A 377 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.37e+00 ... (remaining 19755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 25887 1.29 - 2.58: 668 2.58 - 3.87: 171 3.87 - 5.16: 46 5.16 - 6.46: 32 Bond angle restraints: 26804 Sorted by residual: angle pdb=" CA GLU D 352 " pdb=" CB GLU D 352 " pdb=" CG GLU D 352 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " pdb=" CG GLU C 352 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU B 352 " pdb=" CB GLU B 352 " pdb=" CG GLU B 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU A 352 " pdb=" CB GLU A 352 " pdb=" CG GLU A 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C PHE D 519 " pdb=" N GLN D 520 " pdb=" CA GLN D 520 " ideal model delta sigma weight residual 120.82 124.97 -4.15 1.50e+00 4.44e-01 7.66e+00 ... (remaining 26799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 10459 14.15 - 28.30: 731 28.30 - 42.45: 334 42.45 - 56.60: 44 56.60 - 70.74: 8 Dihedral angle restraints: 11576 sinusoidal: 4620 harmonic: 6956 Sorted by residual: dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU B 345 " pdb=" C LEU B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 11573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2070 0.033 - 0.066: 750 0.066 - 0.100: 192 0.100 - 0.133: 24 0.133 - 0.166: 8 Chirality restraints: 3044 Sorted by residual: chirality pdb=" CA MET A 640 " pdb=" N MET A 640 " pdb=" C MET A 640 " pdb=" CB MET A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA MET C 640 " pdb=" N MET C 640 " pdb=" C MET C 640 " pdb=" CB MET C 640 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA MET B 640 " pdb=" N MET B 640 " pdb=" C MET B 640 " pdb=" CB MET B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3041 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO C 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 148 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4228 2.78 - 3.31: 19254 3.31 - 3.84: 30476 3.84 - 4.37: 33303 4.37 - 4.90: 59116 Nonbonded interactions: 146377 Sorted by model distance: nonbonded pdb=" O PRO A 89 " pdb=" OG1 THR A 93 " model vdw 2.254 3.040 nonbonded pdb=" O PRO D 89 " pdb=" OG1 THR D 93 " model vdw 2.255 3.040 nonbonded pdb=" O PRO C 89 " pdb=" OG1 THR C 93 " model vdw 2.255 3.040 nonbonded pdb=" O PRO B 89 " pdb=" OG1 THR B 93 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP C 258 " pdb=" ND2 ASN C 263 " model vdw 2.292 3.120 ... (remaining 146372 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.200 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.002 0.038 19760 Z= 0.117 Angle : 0.574 6.455 26804 Z= 0.300 Chirality : 0.037 0.166 3044 Planarity : 0.004 0.049 3292 Dihedral : 11.987 70.744 7080 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.19 % Allowed : 0.24 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2348 helix: 1.55 (0.14), residues: 1456 sheet: 2.42 (0.56), residues: 80 loop : -1.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 679 TYR 0.010 0.001 TYR A 271 PHE 0.014 0.001 PHE A 407 TRP 0.009 0.001 TRP A 223 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (19760) covalent geometry : angle 0.57359 / 0.30 (26804) hydrogen bonds : bond 0.14652 / 9.81 ( 1036) hydrogen bonds : angle 4.60963 / 3.24 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 308 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 ASP cc_start: 0.8653 (t70) cc_final: 0.8043 (t0) REVERT: B 536 ASP cc_start: 0.8661 (t70) cc_final: 0.8030 (t0) REVERT: C 536 ASP cc_start: 0.8685 (t70) cc_final: 0.8053 (t0) REVERT: D 536 ASP cc_start: 0.8702 (t70) cc_final: 0.8242 (t0) outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.1259 time to fit residues: 63.1308 Evaluate side-chains 262 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.4806 > 50:) chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN B 263 ASN C 263 ASN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.166423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109794 restraints weight = 29351.865| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.42 r_work: 0.3247 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19760 Z= 0.204 Angle : 0.648 8.974 26804 Z= 0.323 Chirality : 0.041 0.136 3044 Planarity : 0.004 0.043 3292 Dihedral : 3.972 21.914 2588 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.77 % Favored : 90.72 % Rotamer: Outliers : 0.82 % Allowed : 8.03 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2348 helix: 1.38 (0.14), residues: 1440 sheet: 2.10 (0.56), residues: 80 loop : -1.85 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 702 TYR 0.026 0.002 TYR C 471 PHE 0.022 0.002 PHE D 407 TRP 0.008 0.001 TRP C 223 HIS 0.006 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (19760) covalent geometry : angle 0.64825 / 0.32 (26804) hydrogen bonds : bond 0.05038 / 3.40 ( 1036) hydrogen bonds : angle 3.76594 / 2.62 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 284 time to evaluate : 0.805 Fit side-chains REVERT: A 521 HIS cc_start: 0.8446 (m-70) cc_final: 0.7730 (p-80) REVERT: A 645 MET cc_start: 0.8751 (mmm) cc_final: 0.8094 (mmm) REVERT: B 376 GLU cc_start: 0.8144 (tp30) cc_final: 0.7933 (tp30) REVERT: B 464 TRP cc_start: 0.7614 (m100) cc_final: 0.7342 (m100) REVERT: B 521 HIS cc_start: 0.8305 (m-70) cc_final: 0.7574 (p-80) REVERT: B 645 MET cc_start: 0.8802 (mmm) cc_final: 0.8108 (mmm) REVERT: C 234 HIS cc_start: 0.8273 (m90) cc_final: 0.8016 (m90) REVERT: C 376 GLU cc_start: 0.8157 (tp30) cc_final: 0.7956 (tp30) REVERT: C 464 TRP cc_start: 0.7615 (m100) cc_final: 0.7328 (m100) REVERT: C 521 HIS cc_start: 0.8287 (m-70) cc_final: 0.7506 (p-80) REVERT: C 536 ASP cc_start: 0.8557 (t70) cc_final: 0.8353 (t0) REVERT: C 645 MET cc_start: 0.8746 (mmm) cc_final: 0.8084 (mmm) REVERT: D 335 TYR cc_start: 0.8034 (t80) cc_final: 0.7709 (t80) REVERT: D 376 GLU cc_start: 0.8153 (tp30) cc_final: 0.7951 (tp30) REVERT: D 464 TRP cc_start: 0.7641 (m100) cc_final: 0.7360 (m100) REVERT: D 521 HIS cc_start: 0.8245 (m-70) cc_final: 0.7441 (p-80) REVERT: D 536 ASP cc_start: 0.8565 (t70) cc_final: 0.8163 (t0) REVERT: D 645 MET cc_start: 0.8746 (mmm) cc_final: 0.8079 (mmm) outliers start: 17 outliers final: 10 residues processed: 298 average time/residue: 0.1415 time to fit residues: 66.1257 Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 273 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 167 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 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 = 0.4161 r_free = 0.4161 target = 0.165587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109024 restraints weight = 29777.743| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.46 r_work: 0.3240 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19760 Z= 0.181 Angle : 0.621 8.214 26804 Z= 0.308 Chirality : 0.040 0.142 3044 Planarity : 0.004 0.045 3292 Dihedral : 3.998 21.654 2588 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.99 % Favored : 90.33 % Rotamer: Outliers : 0.82 % Allowed : 13.08 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2348 helix: 1.46 (0.14), residues: 1412 sheet: 2.22 (0.56), residues: 80 loop : -1.55 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 702 TYR 0.019 0.001 TYR A 471 PHE 0.015 0.002 PHE B 407 TRP 0.006 0.001 TRP C 223 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (19760) covalent geometry : angle 0.62060 / 0.31 (26804) hydrogen bonds : bond 0.04759 / 3.22 ( 1036) hydrogen bonds : angle 3.68934 / 2.55 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 0.654 Fit side-chains REVERT: A 234 HIS cc_start: 0.8324 (m90) cc_final: 0.8093 (m90) REVERT: A 376 GLU cc_start: 0.8187 (tp30) cc_final: 0.7964 (tp30) REVERT: A 464 TRP cc_start: 0.7619 (m100) cc_final: 0.7353 (m100) REVERT: A 521 HIS cc_start: 0.8413 (m-70) cc_final: 0.7613 (p-80) REVERT: A 536 ASP cc_start: 0.8583 (t0) cc_final: 0.8315 (t0) REVERT: B 234 HIS cc_start: 0.8393 (m90) cc_final: 0.8167 (m90) REVERT: B 349 ASP cc_start: 0.8557 (t0) cc_final: 0.7855 (t70) REVERT: B 376 GLU cc_start: 0.8176 (tp30) cc_final: 0.7929 (tp30) REVERT: B 464 TRP cc_start: 0.7628 (m100) cc_final: 0.7372 (m100) REVERT: B 521 HIS cc_start: 0.8268 (m-70) cc_final: 0.7425 (p-80) REVERT: B 536 ASP cc_start: 0.8558 (t0) cc_final: 0.8299 (t0) REVERT: B 672 GLU cc_start: 0.8889 (tt0) cc_final: 0.8383 (tt0) REVERT: C 234 HIS cc_start: 0.8327 (m90) cc_final: 0.8105 (m90) REVERT: C 349 ASP cc_start: 0.8568 (t0) cc_final: 0.7873 (t70) REVERT: C 376 GLU cc_start: 0.8180 (tp30) cc_final: 0.7935 (tp30) REVERT: C 464 TRP cc_start: 0.7619 (m100) cc_final: 0.7354 (m100) REVERT: C 468 MET cc_start: 0.8000 (mtt) cc_final: 0.7771 (mtp) REVERT: C 521 HIS cc_start: 0.8241 (m-70) cc_final: 0.7373 (p-80) REVERT: C 672 GLU cc_start: 0.8901 (tt0) cc_final: 0.8391 (tt0) REVERT: D 234 HIS cc_start: 0.8328 (m90) cc_final: 0.8099 (m90) REVERT: D 349 ASP cc_start: 0.8560 (t0) cc_final: 0.7858 (t70) REVERT: D 376 GLU cc_start: 0.8176 (tp30) cc_final: 0.7930 (tp30) REVERT: D 464 TRP cc_start: 0.7621 (m100) cc_final: 0.7360 (m100) REVERT: D 521 HIS cc_start: 0.8254 (m-70) cc_final: 0.7362 (p-80) REVERT: D 672 GLU cc_start: 0.8898 (tt0) cc_final: 0.8393 (tt0) outliers start: 17 outliers final: 4 residues processed: 292 average time/residue: 0.1434 time to fit residues: 64.4237 Evaluate side-chains 270 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 41 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 200 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN C 200 GLN D 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110800 restraints weight = 29544.621| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.45 r_work: 0.3265 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19760 Z= 0.128 Angle : 0.588 8.605 26804 Z= 0.289 Chirality : 0.038 0.139 3044 Planarity : 0.004 0.047 3292 Dihedral : 3.887 20.853 2588 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.88 % Favored : 91.44 % Rotamer: Outliers : 0.87 % Allowed : 14.71 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 2348 helix: 1.65 (0.14), residues: 1400 sheet: 2.27 (0.55), residues: 80 loop : -1.56 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 679 TYR 0.026 0.001 TYR A 471 PHE 0.019 0.001 PHE D 540 TRP 0.004 0.001 TRP A 657 HIS 0.007 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19760) covalent geometry : angle 0.58823 / 0.29 (26804) hydrogen bonds : bond 0.04002 / 2.71 ( 1036) hydrogen bonds : angle 3.51029 / 2.44 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 0.737 Fit side-chains REVERT: A 234 HIS cc_start: 0.8373 (m90) cc_final: 0.8157 (m90) REVERT: A 286 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7402 (mm-40) REVERT: A 376 GLU cc_start: 0.8048 (tp30) cc_final: 0.7824 (tp30) REVERT: A 464 TRP cc_start: 0.7616 (m100) cc_final: 0.7352 (m100) REVERT: A 473 GLU cc_start: 0.8207 (mp0) cc_final: 0.7597 (mm-30) REVERT: A 521 HIS cc_start: 0.8436 (m-70) cc_final: 0.7308 (p-80) REVERT: A 525 TYR cc_start: 0.8616 (m-80) cc_final: 0.8126 (m-80) REVERT: A 536 ASP cc_start: 0.8556 (t0) cc_final: 0.7834 (t0) REVERT: A 640 MET cc_start: 0.9106 (tmm) cc_final: 0.8405 (mmp) REVERT: A 654 ASP cc_start: 0.8180 (m-30) cc_final: 0.7704 (p0) REVERT: A 672 GLU cc_start: 0.8480 (tt0) cc_final: 0.8224 (tt0) REVERT: B 234 HIS cc_start: 0.8385 (m90) cc_final: 0.8169 (m90) REVERT: B 286 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7411 (mt0) REVERT: B 376 GLU cc_start: 0.8037 (tp30) cc_final: 0.7787 (tp30) REVERT: B 464 TRP cc_start: 0.7630 (m100) cc_final: 0.7371 (m100) REVERT: B 473 GLU cc_start: 0.8217 (mp0) cc_final: 0.7583 (mm-30) REVERT: B 521 HIS cc_start: 0.8294 (m-70) cc_final: 0.7124 (p-80) REVERT: B 525 TYR cc_start: 0.8610 (m-80) cc_final: 0.8151 (m-80) REVERT: B 536 ASP cc_start: 0.8548 (t0) cc_final: 0.7842 (t0) REVERT: B 640 MET cc_start: 0.9077 (tmm) cc_final: 0.8360 (mmp) REVERT: C 234 HIS cc_start: 0.8354 (m90) cc_final: 0.8146 (m90) REVERT: C 286 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7411 (mm-40) REVERT: C 376 GLU cc_start: 0.8040 (tp30) cc_final: 0.7794 (tp30) REVERT: C 464 TRP cc_start: 0.7608 (m100) cc_final: 0.7342 (m100) REVERT: C 473 GLU cc_start: 0.8220 (mp0) cc_final: 0.7601 (mm-30) REVERT: C 521 HIS cc_start: 0.8299 (m-70) cc_final: 0.8019 (m-70) REVERT: C 525 TYR cc_start: 0.8613 (m-80) cc_final: 0.8118 (m-80) REVERT: C 536 ASP cc_start: 0.8483 (t0) cc_final: 0.8087 (t0) REVERT: C 640 MET cc_start: 0.9042 (tmm) cc_final: 0.8296 (mmp) REVERT: D 234 HIS cc_start: 0.8350 (m90) cc_final: 0.8136 (m90) REVERT: D 376 GLU cc_start: 0.8024 (tp30) cc_final: 0.7772 (tp30) REVERT: D 464 TRP cc_start: 0.7638 (m100) cc_final: 0.7379 (m100) REVERT: D 473 GLU cc_start: 0.8222 (mp0) cc_final: 0.7574 (mm-30) REVERT: D 521 HIS cc_start: 0.8293 (m-70) cc_final: 0.8006 (m-70) REVERT: D 525 TYR cc_start: 0.8601 (m-80) cc_final: 0.8102 (m-80) REVERT: D 536 ASP cc_start: 0.8544 (t0) cc_final: 0.8273 (t70) REVERT: D 640 MET cc_start: 0.9193 (tmm) cc_final: 0.8452 (mmp) REVERT: D 645 MET cc_start: 0.8706 (mmm) cc_final: 0.8340 (tpt) outliers start: 18 outliers final: 8 residues processed: 290 average time/residue: 0.1359 time to fit residues: 62.1134 Evaluate side-chains 279 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 271 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 363 HIS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 363 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 232 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN C 186 ASN D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.165263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108602 restraints weight = 29474.497| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.47 r_work: 0.3230 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19760 Z= 0.160 Angle : 0.603 9.568 26804 Z= 0.299 Chirality : 0.039 0.143 3044 Planarity : 0.004 0.047 3292 Dihedral : 3.960 21.824 2588 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.90 % Favored : 90.42 % Rotamer: Outliers : 1.06 % Allowed : 15.72 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2348 helix: 1.54 (0.14), residues: 1412 sheet: 2.24 (0.55), residues: 80 loop : -1.56 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 679 TYR 0.024 0.001 TYR C 471 PHE 0.019 0.001 PHE C 540 TRP 0.004 0.001 TRP D 386 HIS 0.005 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (19760) covalent geometry : angle 0.60273 / 0.30 (26804) hydrogen bonds : bond 0.04403 / 2.98 ( 1036) hydrogen bonds : angle 3.60439 / 2.51 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.792 Fit side-chains REVERT: A 234 HIS cc_start: 0.8473 (m90) cc_final: 0.8269 (m90) REVERT: A 286 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7477 (mt0) REVERT: A 376 GLU cc_start: 0.8170 (tp30) cc_final: 0.7912 (tp30) REVERT: A 464 TRP cc_start: 0.7650 (m100) cc_final: 0.7389 (m100) REVERT: A 521 HIS cc_start: 0.8514 (m-70) cc_final: 0.7337 (p-80) REVERT: A 525 TYR cc_start: 0.8686 (m-80) cc_final: 0.8189 (m-80) REVERT: A 536 ASP cc_start: 0.8521 (t0) cc_final: 0.7797 (t0) REVERT: A 640 MET cc_start: 0.9131 (tmm) cc_final: 0.8298 (mmp) REVERT: B 234 HIS cc_start: 0.8468 (m90) cc_final: 0.8253 (m90) REVERT: B 376 GLU cc_start: 0.8179 (tp30) cc_final: 0.7921 (tp30) REVERT: B 464 TRP cc_start: 0.7632 (m100) cc_final: 0.7378 (m100) REVERT: B 521 HIS cc_start: 0.8371 (m-70) cc_final: 0.7228 (p-80) REVERT: B 525 TYR cc_start: 0.8681 (m-80) cc_final: 0.8190 (m-80) REVERT: B 536 ASP cc_start: 0.8572 (t0) cc_final: 0.7842 (t0) REVERT: B 640 MET cc_start: 0.9116 (tmm) cc_final: 0.8258 (mmp) REVERT: B 654 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8159 (t0) REVERT: C 234 HIS cc_start: 0.8462 (m90) cc_final: 0.8262 (m90) REVERT: C 286 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7487 (mt0) REVERT: C 376 GLU cc_start: 0.8176 (tp30) cc_final: 0.7921 (tp30) REVERT: C 464 TRP cc_start: 0.7655 (m100) cc_final: 0.7392 (m100) REVERT: C 521 HIS cc_start: 0.8367 (m-70) cc_final: 0.8121 (m-70) REVERT: C 525 TYR cc_start: 0.8660 (m-80) cc_final: 0.8182 (m-80) REVERT: C 536 ASP cc_start: 0.8487 (t0) cc_final: 0.8065 (t70) REVERT: C 640 MET cc_start: 0.9037 (tmm) cc_final: 0.8239 (mmp) REVERT: D 234 HIS cc_start: 0.8467 (m90) cc_final: 0.8262 (m90) REVERT: D 286 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7471 (mt0) REVERT: D 376 GLU cc_start: 0.8168 (tp30) cc_final: 0.7911 (tp30) REVERT: D 464 TRP cc_start: 0.7676 (m100) cc_final: 0.7421 (m100) REVERT: D 521 HIS cc_start: 0.8316 (m-70) cc_final: 0.8052 (m-70) REVERT: D 525 TYR cc_start: 0.8675 (m-80) cc_final: 0.8192 (m-80) REVERT: D 536 ASP cc_start: 0.8598 (t0) cc_final: 0.8027 (t70) REVERT: D 640 MET cc_start: 0.9191 (tmm) cc_final: 0.8288 (mmp) REVERT: D 683 HIS cc_start: 0.8381 (t-90) cc_final: 0.8000 (t-90) outliers start: 22 outliers final: 12 residues processed: 289 average time/residue: 0.1374 time to fit residues: 62.2020 Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 363 HIS Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 182 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 613 GLN C 613 GLN D 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111614 restraints weight = 29398.580| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.46 r_work: 0.3279 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19760 Z= 0.111 Angle : 0.566 8.246 26804 Z= 0.277 Chirality : 0.037 0.150 3044 Planarity : 0.003 0.047 3292 Dihedral : 3.841 20.359 2588 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.75 % Favored : 91.57 % Rotamer: Outliers : 0.72 % Allowed : 17.12 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 2348 helix: 1.69 (0.14), residues: 1416 sheet: 2.22 (0.54), residues: 80 loop : -1.50 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 679 TYR 0.009 0.001 TYR D 271 PHE 0.031 0.001 PHE D 540 TRP 0.004 0.001 TRP A 657 HIS 0.004 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (19760) covalent geometry : angle 0.56558 / 0.28 (26804) hydrogen bonds : bond 0.03601 / 2.44 ( 1036) hydrogen bonds : angle 3.44452 / 2.40 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7398 (mt0) REVERT: A 464 TRP cc_start: 0.7607 (m100) cc_final: 0.7350 (m100) REVERT: A 525 TYR cc_start: 0.8628 (m-80) cc_final: 0.8145 (m-80) REVERT: A 536 ASP cc_start: 0.8494 (t0) cc_final: 0.7929 (t0) REVERT: A 640 MET cc_start: 0.9092 (tmm) cc_final: 0.8299 (mmp) REVERT: A 645 MET cc_start: 0.8704 (mmm) cc_final: 0.8440 (mmm) REVERT: A 654 ASP cc_start: 0.8441 (m-30) cc_final: 0.7671 (p0) REVERT: B 286 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7405 (mt0) REVERT: B 335 TYR cc_start: 0.8351 (t80) cc_final: 0.7479 (t80) REVERT: B 464 TRP cc_start: 0.7600 (m100) cc_final: 0.7339 (m100) REVERT: B 525 TYR cc_start: 0.8648 (m-80) cc_final: 0.8242 (m-80) REVERT: B 536 ASP cc_start: 0.8520 (t0) cc_final: 0.7956 (t0) REVERT: B 640 MET cc_start: 0.9090 (tmm) cc_final: 0.8303 (mmp) REVERT: B 654 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8208 (t0) REVERT: C 286 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7398 (mt0) REVERT: C 464 TRP cc_start: 0.7630 (m100) cc_final: 0.7373 (m100) REVERT: C 525 TYR cc_start: 0.8621 (m-80) cc_final: 0.8149 (m-80) REVERT: C 536 ASP cc_start: 0.8422 (t0) cc_final: 0.7983 (t0) REVERT: C 640 MET cc_start: 0.8996 (tmm) cc_final: 0.8245 (mmp) REVERT: D 286 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7402 (mt0) REVERT: D 464 TRP cc_start: 0.7641 (m100) cc_final: 0.7390 (m100) REVERT: D 525 TYR cc_start: 0.8619 (m-80) cc_final: 0.8146 (m-80) REVERT: D 536 ASP cc_start: 0.8561 (t0) cc_final: 0.8207 (t70) REVERT: D 640 MET cc_start: 0.9192 (tmm) cc_final: 0.8367 (mmp) outliers start: 15 outliers final: 8 residues processed: 289 average time/residue: 0.1381 time to fit residues: 62.6274 Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 263 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 363 HIS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 363 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 35 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN B 165 HIS C 186 ASN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.164032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107330 restraints weight = 29806.685| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.47 r_work: 0.3216 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19760 Z= 0.184 Angle : 0.632 9.424 26804 Z= 0.313 Chirality : 0.039 0.149 3044 Planarity : 0.004 0.047 3292 Dihedral : 3.991 22.037 2588 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.82 % Favored : 90.50 % Rotamer: Outliers : 1.25 % Allowed : 17.84 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2348 helix: 1.59 (0.14), residues: 1400 sheet: 2.23 (0.55), residues: 80 loop : -1.59 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 679 TYR 0.011 0.001 TYR C 335 PHE 0.026 0.002 PHE B 540 TRP 0.004 0.001 TRP D 386 HIS 0.006 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (19760) covalent geometry : angle 0.63163 / 0.31 (26804) hydrogen bonds : bond 0.04630 / 3.13 ( 1036) hydrogen bonds : angle 3.64421 / 2.54 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.736 Fit side-chains REVERT: A 286 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7509 (mt0) REVERT: A 349 ASP cc_start: 0.8575 (t0) cc_final: 0.8073 (t70) REVERT: A 376 GLU cc_start: 0.8249 (tp30) cc_final: 0.8013 (tp30) REVERT: A 464 TRP cc_start: 0.7649 (m100) cc_final: 0.7393 (m100) REVERT: A 473 GLU cc_start: 0.8301 (mp0) cc_final: 0.7753 (mm-30) REVERT: A 525 TYR cc_start: 0.8693 (m-80) cc_final: 0.8195 (m-80) REVERT: A 536 ASP cc_start: 0.8490 (t0) cc_final: 0.7870 (t0) REVERT: A 640 MET cc_start: 0.9122 (tmm) cc_final: 0.8238 (mmp) REVERT: A 654 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 672 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: A 683 HIS cc_start: 0.8365 (t-90) cc_final: 0.7935 (t-90) REVERT: B 286 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7503 (mt0) REVERT: B 376 GLU cc_start: 0.8267 (tp30) cc_final: 0.8023 (tp30) REVERT: B 464 TRP cc_start: 0.7632 (m100) cc_final: 0.7381 (m100) REVERT: B 473 GLU cc_start: 0.8324 (mp0) cc_final: 0.7756 (mm-30) REVERT: B 525 TYR cc_start: 0.8779 (m-80) cc_final: 0.8216 (m-80) REVERT: B 536 ASP cc_start: 0.8496 (t0) cc_final: 0.8061 (t0) REVERT: B 645 MET cc_start: 0.8486 (mmm) cc_final: 0.8136 (tpt) REVERT: B 654 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 683 HIS cc_start: 0.8352 (t-90) cc_final: 0.7916 (t-90) REVERT: C 286 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7522 (mt0) REVERT: C 376 GLU cc_start: 0.8265 (tp30) cc_final: 0.8020 (tp30) REVERT: C 464 TRP cc_start: 0.7683 (m100) cc_final: 0.7426 (m100) REVERT: C 473 GLU cc_start: 0.8286 (mp0) cc_final: 0.7745 (mm-30) REVERT: C 525 TYR cc_start: 0.8698 (m-80) cc_final: 0.8276 (m-80) REVERT: C 536 ASP cc_start: 0.8491 (t0) cc_final: 0.8105 (t0) REVERT: C 654 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (t0) REVERT: C 683 HIS cc_start: 0.8389 (t-90) cc_final: 0.7955 (t-90) REVERT: D 286 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7508 (mt0) REVERT: D 376 GLU cc_start: 0.8260 (tp30) cc_final: 0.8020 (tp30) REVERT: D 464 TRP cc_start: 0.7679 (m100) cc_final: 0.7429 (m100) REVERT: D 473 GLU cc_start: 0.8315 (mp0) cc_final: 0.7746 (mm-30) REVERT: D 525 TYR cc_start: 0.8686 (m-80) cc_final: 0.8261 (m-80) REVERT: D 536 ASP cc_start: 0.8531 (t0) cc_final: 0.8324 (t70) REVERT: D 640 MET cc_start: 0.9211 (tmm) cc_final: 0.8980 (tmm) REVERT: D 654 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8170 (t0) REVERT: D 683 HIS cc_start: 0.8354 (t-90) cc_final: 0.7936 (t-90) outliers start: 26 outliers final: 14 residues processed: 283 average time/residue: 0.1457 time to fit residues: 63.5913 Evaluate side-chains 286 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 363 HIS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 222 optimal weight: 0.0050 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN D 663 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112733 restraints weight = 29588.578| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.46 r_work: 0.3299 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19760 Z= 0.105 Angle : 0.572 10.168 26804 Z= 0.280 Chirality : 0.037 0.170 3044 Planarity : 0.003 0.047 3292 Dihedral : 3.818 19.581 2588 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.84 % Favored : 91.57 % Rotamer: Outliers : 0.62 % Allowed : 18.75 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 2348 helix: 1.77 (0.14), residues: 1416 sheet: 2.24 (0.54), residues: 80 loop : -1.47 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 679 TYR 0.008 0.001 TYR D 335 PHE 0.029 0.001 PHE B 540 TRP 0.005 0.001 TRP A 657 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (19760) covalent geometry : angle 0.57158 / 0.28 (26804) hydrogen bonds : bond 0.03315 / 2.25 ( 1036) hydrogen bonds : angle 3.39983 / 2.37 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 286 time to evaluate : 0.829 Fit side-chains REVERT: A 286 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7381 (mt0) REVERT: A 349 ASP cc_start: 0.8417 (t0) cc_final: 0.7837 (t70) REVERT: A 464 TRP cc_start: 0.7560 (m100) cc_final: 0.7293 (m100) REVERT: A 471 TYR cc_start: 0.7677 (p90) cc_final: 0.7446 (p90) REVERT: A 525 TYR cc_start: 0.8617 (m-80) cc_final: 0.8136 (m-80) REVERT: A 536 ASP cc_start: 0.8459 (t0) cc_final: 0.7855 (t0) REVERT: A 640 MET cc_start: 0.9117 (tmm) cc_final: 0.8253 (mmp) REVERT: A 672 GLU cc_start: 0.8875 (tt0) cc_final: 0.8384 (pt0) REVERT: B 286 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7379 (mt0) REVERT: B 464 TRP cc_start: 0.7554 (m100) cc_final: 0.7293 (m100) REVERT: B 525 TYR cc_start: 0.8625 (m-80) cc_final: 0.8209 (m-80) REVERT: B 536 ASP cc_start: 0.8522 (t0) cc_final: 0.8035 (t0) REVERT: B 645 MET cc_start: 0.8394 (mmm) cc_final: 0.8188 (tpt) REVERT: B 654 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8173 (t0) REVERT: C 286 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7382 (mt0) REVERT: C 464 TRP cc_start: 0.7651 (m100) cc_final: 0.7388 (m100) REVERT: C 471 TYR cc_start: 0.7692 (p90) cc_final: 0.7305 (p90) REVERT: C 525 TYR cc_start: 0.8694 (m-80) cc_final: 0.8265 (m-80) REVERT: C 536 ASP cc_start: 0.8485 (t0) cc_final: 0.8135 (t0) REVERT: C 640 MET cc_start: 0.9106 (tmm) cc_final: 0.8823 (tmm) REVERT: D 286 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7377 (mt0) REVERT: D 464 TRP cc_start: 0.7591 (m100) cc_final: 0.7332 (m100) REVERT: D 471 TYR cc_start: 0.7661 (p90) cc_final: 0.7390 (p90) REVERT: D 525 TYR cc_start: 0.8677 (m-80) cc_final: 0.8233 (m-80) REVERT: D 536 ASP cc_start: 0.8486 (t0) cc_final: 0.8055 (t0) REVERT: D 640 MET cc_start: 0.9188 (tmm) cc_final: 0.8870 (tmm) REVERT: D 683 HIS cc_start: 0.8309 (t-90) cc_final: 0.8004 (t-90) outliers start: 13 outliers final: 10 residues processed: 293 average time/residue: 0.1366 time to fit residues: 63.1706 Evaluate side-chains 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 408 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 210 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 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 = 0.4150 r_free = 0.4150 target = 0.164753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108053 restraints weight = 29500.284| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.45 r_work: 0.3229 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19760 Z= 0.171 Angle : 0.661 14.230 26804 Z= 0.317 Chirality : 0.039 0.178 3044 Planarity : 0.004 0.047 3292 Dihedral : 3.935 22.002 2588 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Rotamer: Outliers : 1.35 % Allowed : 18.51 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2348 helix: 1.64 (0.14), residues: 1400 sheet: 2.24 (0.54), residues: 80 loop : -1.60 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 679 TYR 0.012 0.001 TYR C 271 PHE 0.027 0.002 PHE A 540 TRP 0.004 0.001 TRP C 386 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (19760) covalent geometry : angle 0.66075 / 0.32 (26804) hydrogen bonds : bond 0.04396 / 2.98 ( 1036) hydrogen bonds : angle 3.60159 / 2.51 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.770 Fit side-chains REVERT: A 286 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7490 (mt0) REVERT: A 349 ASP cc_start: 0.8534 (t0) cc_final: 0.8002 (t70) REVERT: A 376 GLU cc_start: 0.8203 (tp30) cc_final: 0.7974 (tp30) REVERT: A 464 TRP cc_start: 0.7622 (m100) cc_final: 0.7359 (m100) REVERT: A 525 TYR cc_start: 0.8668 (m-80) cc_final: 0.8192 (m-80) REVERT: A 536 ASP cc_start: 0.8482 (t0) cc_final: 0.8028 (t0) REVERT: A 672 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: A 683 HIS cc_start: 0.8379 (t-90) cc_final: 0.7957 (t-90) REVERT: B 174 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8873 (mmmt) REVERT: B 286 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7475 (mt0) REVERT: B 376 GLU cc_start: 0.8234 (tp30) cc_final: 0.7977 (tp30) REVERT: B 464 TRP cc_start: 0.7618 (m100) cc_final: 0.7351 (m100) REVERT: B 471 TYR cc_start: 0.7870 (p90) cc_final: 0.7462 (p90) REVERT: B 525 TYR cc_start: 0.8766 (m-80) cc_final: 0.8301 (m-80) REVERT: B 536 ASP cc_start: 0.8512 (t0) cc_final: 0.8087 (t0) REVERT: B 640 MET cc_start: 0.9177 (tmm) cc_final: 0.8874 (tmm) REVERT: B 654 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8160 (t0) REVERT: B 683 HIS cc_start: 0.8417 (t-90) cc_final: 0.7999 (t-90) REVERT: C 174 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8892 (mmmt) REVERT: C 286 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7481 (mt0) REVERT: C 376 GLU cc_start: 0.8245 (tp30) cc_final: 0.7989 (tp30) REVERT: C 464 TRP cc_start: 0.7695 (m100) cc_final: 0.7436 (m100) REVERT: C 525 TYR cc_start: 0.8798 (m-80) cc_final: 0.8342 (m-80) REVERT: C 536 ASP cc_start: 0.8503 (t0) cc_final: 0.8120 (t0) REVERT: C 640 MET cc_start: 0.9121 (tmm) cc_final: 0.8854 (tmm) REVERT: C 683 HIS cc_start: 0.8412 (t-90) cc_final: 0.7993 (t-90) REVERT: D 286 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7485 (mt0) REVERT: D 376 GLU cc_start: 0.8234 (tp30) cc_final: 0.7977 (tp30) REVERT: D 464 TRP cc_start: 0.7648 (m100) cc_final: 0.7385 (m100) REVERT: D 525 TYR cc_start: 0.8792 (m-80) cc_final: 0.8246 (m-80) REVERT: D 536 ASP cc_start: 0.8448 (t0) cc_final: 0.7989 (t0) REVERT: D 640 MET cc_start: 0.9193 (tmm) cc_final: 0.8925 (tmm) REVERT: D 683 HIS cc_start: 0.8362 (t-90) cc_final: 0.7936 (t-90) outliers start: 28 outliers final: 20 residues processed: 292 average time/residue: 0.1443 time to fit residues: 65.4720 Evaluate side-chains 290 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 363 HIS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 363 HIS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 363 HIS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 127 optimal weight: 0.0170 chunk 74 optimal weight: 5.9990 chunk 114 optimal weight: 0.0770 chunk 90 optimal weight: 0.8980 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 663 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.169530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113476 restraints weight = 29704.805| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.46 r_work: 0.3311 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19760 Z= 0.105 Angle : 0.595 12.403 26804 Z= 0.285 Chirality : 0.037 0.182 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.772 19.181 2588 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.79 % Favored : 91.70 % Rotamer: Outliers : 0.91 % Allowed : 19.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2348 helix: 1.81 (0.14), residues: 1412 sheet: 1.74 (0.56), residues: 88 loop : -1.46 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 679 TYR 0.008 0.001 TYR D 634 PHE 0.026 0.001 PHE A 540 TRP 0.005 0.001 TRP A 657 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (19760) covalent geometry : angle 0.59488 / 0.28 (26804) hydrogen bonds : bond 0.03140 / 2.12 ( 1036) hydrogen bonds : angle 3.43182 / 2.39 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 278 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7382 (mt0) REVERT: A 464 TRP cc_start: 0.7517 (m100) cc_final: 0.7251 (m100) REVERT: A 525 TYR cc_start: 0.8621 (m-80) cc_final: 0.8137 (m-80) REVERT: A 536 ASP cc_start: 0.8543 (t0) cc_final: 0.8125 (t0) REVERT: A 640 MET cc_start: 0.9170 (tmm) cc_final: 0.8843 (tmm) REVERT: B 174 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8892 (mmmt) REVERT: B 186 ASN cc_start: 0.8060 (m110) cc_final: 0.7833 (m110) REVERT: B 286 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7380 (mt0) REVERT: B 464 TRP cc_start: 0.7518 (m100) cc_final: 0.7256 (m100) REVERT: B 525 TYR cc_start: 0.8781 (m-80) cc_final: 0.8167 (m-80) REVERT: B 536 ASP cc_start: 0.8505 (t0) cc_final: 0.8055 (t0) REVERT: B 640 MET cc_start: 0.9147 (tmm) cc_final: 0.8811 (tmm) REVERT: B 672 GLU cc_start: 0.8885 (tt0) cc_final: 0.8666 (tt0) REVERT: C 174 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8898 (mmmt) REVERT: C 286 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7377 (mt0) REVERT: C 464 TRP cc_start: 0.7636 (m100) cc_final: 0.7375 (m100) REVERT: C 525 TYR cc_start: 0.8746 (m-80) cc_final: 0.8220 (m-80) REVERT: C 640 MET cc_start: 0.9137 (tmm) cc_final: 0.8932 (tmm) REVERT: C 672 GLU cc_start: 0.8892 (tt0) cc_final: 0.8675 (tt0) REVERT: C 683 HIS cc_start: 0.8310 (t-90) cc_final: 0.8021 (t-90) REVERT: D 286 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7381 (mt0) REVERT: D 464 TRP cc_start: 0.7544 (m100) cc_final: 0.7288 (m100) REVERT: D 525 TYR cc_start: 0.8696 (m-80) cc_final: 0.8311 (m-80) REVERT: D 528 MET cc_start: 0.8025 (ppp) cc_final: 0.7747 (ptp) REVERT: D 536 ASP cc_start: 0.8460 (t0) cc_final: 0.8012 (t0) REVERT: D 640 MET cc_start: 0.9159 (tmm) cc_final: 0.8875 (tmm) REVERT: D 654 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8162 (t0) REVERT: D 672 GLU cc_start: 0.8897 (tt0) cc_final: 0.8653 (tt0) outliers start: 19 outliers final: 16 residues processed: 289 average time/residue: 0.1387 time to fit residues: 63.2809 Evaluate side-chains 288 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 172 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 227 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** D 186 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 = 0.4194 r_free = 0.4194 target = 0.168790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112534 restraints weight = 29582.736| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.48 r_work: 0.3288 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19760 Z= 0.108 Angle : 0.604 14.075 26804 Z= 0.287 Chirality : 0.037 0.180 3044 Planarity : 0.003 0.047 3292 Dihedral : 3.710 20.044 2588 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.50 % Favored : 91.99 % Rotamer: Outliers : 1.11 % Allowed : 19.18 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2348 helix: 1.86 (0.14), residues: 1400 sheet: 1.86 (0.56), residues: 88 loop : -1.49 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 679 TYR 0.009 0.001 TYR D 335 PHE 0.026 0.001 PHE A 540 TRP 0.005 0.001 TRP B 509 HIS 0.004 0.001 HIS C 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (19760) covalent geometry : angle 0.60411 / 0.29 (26804) hydrogen bonds : bond 0.03303 / 2.23 ( 1036) hydrogen bonds : angle 3.43988 / 2.40 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5645.26 seconds wall clock time: 97 minutes 15.03 seconds (5835.03 seconds total)