Starting phenix.real_space_refine on Fri Sep 19 12:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x5f_6707/09_2025/5x5f_6707.map" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 153 5.16 5 C 16799 2.51 5 N 4372 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26422 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "C" Number of atoms: 8810 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8804 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 1141, 8804 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 8997 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 10.17, per 1000 atoms: 0.38 Number of scatterers: 26422 At special positions: 0 Unit cell: (152.1, 159.9, 189.8, 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 153 16.00 O 5098 8.00 N 4372 7.00 C 16799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.05 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.62 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.01 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.01 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.06 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.46 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.71 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.02 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.01 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.678A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.471A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.972A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.718A pdb=" N SER A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1018 through 1041 Processing helix chain 'A' and resid 1062 through 1107 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.678A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.640A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.470A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.974A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.716A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1011 Processing helix chain 'B' and resid 1018 through 1041 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.373A pdb=" N ASP B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.607A pdb=" N SER C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.971A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1018 through 1041 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.061A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 4.072A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.860A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.879A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.599A pdb=" N LEU A 441 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.070A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE A 782 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1122 through 1124 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.108A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.548A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.879A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.789A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.072A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.563A pdb=" N ILE B 782 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AD5, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.250A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.069A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.856A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.877A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.787A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'C' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE C 782 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 803 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1122 through 1124 841 hydrogen bonds defined for protein. 2241 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: 5.36 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4327 1.29 - 1.43: 7452 1.43 - 1.57: 15019 1.57 - 1.70: 28 1.70 - 1.84: 199 Bond restraints: 27025 Sorted by residual: bond pdb=" N CYS A 349 " pdb=" CA CYS A 349 " ideal model delta sigma weight residual 1.459 1.156 0.303 1.19e-02 7.06e+03 6.48e+02 bond pdb=" C CYS A 349 " pdb=" O CYS A 349 " ideal model delta sigma weight residual 1.236 1.411 -0.175 1.15e-02 7.56e+03 2.31e+02 bond pdb=" N MET A 696 " pdb=" CA MET A 696 " ideal model delta sigma weight residual 1.456 1.592 -0.136 1.50e-02 4.44e+03 8.26e+01 bond pdb=" CA CYS A 349 " pdb=" CB CYS A 349 " ideal model delta sigma weight residual 1.529 1.638 -0.109 1.55e-02 4.16e+03 4.92e+01 bond pdb=" N ARG B 822 " pdb=" CA ARG B 822 " ideal model delta sigma weight residual 1.458 1.548 -0.090 1.30e-02 5.92e+03 4.84e+01 ... (remaining 27020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 36091 5.14 - 10.28: 527 10.28 - 15.42: 102 15.42 - 20.56: 26 20.56 - 25.70: 3 Bond angle restraints: 36749 Sorted by residual: angle pdb=" O CYS A 349 " pdb=" C CYS A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 122.07 104.98 17.09 1.03e+00 9.43e-01 2.75e+02 angle pdb=" N CYS A 349 " pdb=" CA CYS A 349 " pdb=" C CYS A 349 " ideal model delta sigma weight residual 111.07 94.92 16.15 1.07e+00 8.73e-01 2.28e+02 angle pdb=" N ASN A 406 " pdb=" CA ASN A 406 " pdb=" C ASN A 406 " ideal model delta sigma weight residual 113.72 96.18 17.54 1.52e+00 4.33e-01 1.33e+02 angle pdb=" CA CYS A 349 " pdb=" C CYS A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 117.07 129.37 -12.30 1.14e+00 7.69e-01 1.16e+02 angle pdb=" C CYS A 349 " pdb=" N SER A 350 " pdb=" CA SER A 350 " ideal model delta sigma weight residual 121.50 136.82 -15.32 1.43e+00 4.89e-01 1.15e+02 ... (remaining 36744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15398 26.90 - 53.79: 593 53.79 - 80.69: 67 80.69 - 107.58: 10 107.58 - 134.48: 9 Dihedral angle restraints: 16077 sinusoidal: 6087 harmonic: 9990 Sorted by residual: dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.52 -134.48 0 5.00e+00 4.00e-02 7.23e+02 dihedral pdb=" CA SER C 856 " pdb=" C SER C 856 " pdb=" N GLN C 857 " pdb=" CA GLN C 857 " ideal model delta harmonic sigma weight residual -180.00 -45.64 -134.36 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.65 -134.35 0 5.00e+00 4.00e-02 7.22e+02 ... (remaining 16074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 3998 0.192 - 0.384: 120 0.384 - 0.576: 10 0.576 - 0.767: 1 0.767 - 0.959: 2 Chirality restraints: 4131 Sorted by residual: chirality pdb=" CA ASN A 582 " pdb=" N ASN A 582 " pdb=" C ASN A 582 " pdb=" CB ASN A 582 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA GLN B 627 " pdb=" N GLN B 627 " pdb=" C GLN B 627 " pdb=" CB GLN B 627 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA ARG C1057 " pdb=" N ARG C1057 " pdb=" C ARG C1057 " pdb=" CB ARG C1057 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.99e+00 ... (remaining 4128 not shown) Planarity restraints: 4750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 520 " -0.038 2.00e-02 2.50e+03 8.03e-02 6.44e+01 pdb=" C ALA A 520 " 0.139 2.00e-02 2.50e+03 pdb=" O ALA A 520 " -0.055 2.00e-02 2.50e+03 pdb=" N ASN A 521 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.025 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" CD GLN C 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN C 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN C 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" CD GLN B 280 " 0.090 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " -0.032 2.00e-02 2.50e+03 ... (remaining 4747 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 75 2.13 - 2.82: 8582 2.82 - 3.51: 36003 3.51 - 4.21: 66498 4.21 - 4.90: 109792 Nonbonded interactions: 220950 Sorted by model distance: nonbonded pdb=" O GLN B 427 " pdb=" O ARG C1057 " model vdw 1.433 3.040 nonbonded pdb=" O ASP B 510 " pdb=" ND2 ASN C 436 " model vdw 1.454 3.120 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 1.465 3.040 nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 1.465 3.040 nonbonded pdb=" OH TYR A 58 " pdb=" O GLY A 331 " model vdw 1.466 3.040 ... (remaining 220945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 59 or (resid 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 1206)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.200 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 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 : 0.013 0.676 27065 Z= 0.718 Angle : 1.814 54.824 36821 Z= 1.026 Chirality : 0.085 0.959 4131 Planarity : 0.009 0.114 4750 Dihedral : 14.738 134.478 9585 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 32.72 Ramachandran Plot: Outliers : 1.42 % Allowed : 13.04 % Favored : 85.54 % Rotamer: Outliers : 5.99 % Allowed : 7.29 % Favored : 86.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.28 % Twisted Proline : 0.00 % Twisted General : 1.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.12), residues: 3390 helix: -2.88 (0.14), residues: 682 sheet: -1.15 (0.21), residues: 572 loop : -2.96 (0.11), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 119 TYR 0.046 0.004 TYR B1171 PHE 0.038 0.004 PHE A1172 TRP 0.032 0.005 TRP A 960 HIS 0.017 0.004 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.01090 (27025) covalent geometry : angle 1.70189 (36749) SS BOND : bond 0.16596 ( 36) SS BOND : angle 14.32283 ( 72) hydrogen bonds : bond 0.16023 ( 841) hydrogen bonds : angle 10.57574 ( 2241) Misc. bond : bond 0.25949 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 672 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: A 127 THR cc_start: 0.6987 (m) cc_final: 0.6314 (p) REVERT: A 346 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8313 (tp-100) REVERT: A 361 TYR cc_start: 0.8238 (m-80) cc_final: 0.7949 (m-80) REVERT: A 487 ASN cc_start: 0.1989 (OUTLIER) cc_final: 0.0888 (t0) REVERT: A 493 LYS cc_start: -0.5398 (OUTLIER) cc_final: -0.6187 (mmtm) REVERT: A 581 THR cc_start: 0.6070 (OUTLIER) cc_final: 0.5772 (m) REVERT: A 786 PHE cc_start: 0.8146 (m-80) cc_final: 0.7921 (m-10) REVERT: A 819 GLN cc_start: 0.8843 (mt0) cc_final: 0.8394 (tp40) REVERT: A 891 GLU cc_start: 0.8901 (tt0) cc_final: 0.8653 (tt0) REVERT: A 943 MET cc_start: 0.7547 (ttp) cc_final: 0.7347 (ttp) REVERT: A 1015 THR cc_start: 0.8231 (p) cc_final: 0.7979 (t) REVERT: A 1061 LEU cc_start: 0.7076 (mt) cc_final: 0.6705 (mm) REVERT: A 1086 LEU cc_start: 0.9212 (mt) cc_final: 0.8841 (mp) REVERT: B 353 SER cc_start: 0.7568 (OUTLIER) cc_final: 0.7367 (t) REVERT: B 438 TYR cc_start: 0.1159 (OUTLIER) cc_final: 0.0245 (m-80) REVERT: B 511 ARG cc_start: 0.0163 (OUTLIER) cc_final: -0.0237 (mpt-90) REVERT: B 609 TYR cc_start: 0.3474 (OUTLIER) cc_final: 0.3160 (p90) REVERT: B 724 VAL cc_start: 0.5399 (OUTLIER) cc_final: 0.5198 (p) REVERT: B 830 LYS cc_start: 0.9214 (mttt) cc_final: 0.8991 (ptpt) REVERT: B 928 TYR cc_start: 0.7184 (m-80) cc_final: 0.6883 (m-10) REVERT: B 993 ASN cc_start: 0.8544 (m-40) cc_final: 0.7792 (p0) REVERT: B 1017 GLU cc_start: 0.8449 (pm20) cc_final: 0.8232 (pp20) REVERT: B 1082 VAL cc_start: 0.9532 (t) cc_final: 0.9146 (p) REVERT: B 1086 LEU cc_start: 0.9272 (mt) cc_final: 0.8984 (mp) REVERT: B 1172 PHE cc_start: 0.8312 (m-80) cc_final: 0.7812 (m-80) REVERT: C 58 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.6041 (t80) REVERT: C 367 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6832 (pp20) REVERT: C 564 THR cc_start: 0.0440 (OUTLIER) cc_final: 0.0145 (m) REVERT: C 655 VAL cc_start: 0.7770 (t) cc_final: 0.7529 (m) REVERT: C 659 VAL cc_start: 0.7715 (p) cc_final: 0.7163 (p) REVERT: C 697 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.5969 (tp) REVERT: C 843 ASP cc_start: 0.8164 (m-30) cc_final: 0.7887 (m-30) REVERT: C 892 ASP cc_start: 0.9010 (m-30) cc_final: 0.8727 (m-30) REVERT: C 1042 ASN cc_start: 0.7622 (p0) cc_final: 0.7356 (p0) REVERT: C 1064 ASP cc_start: 0.8434 (m-30) cc_final: 0.8147 (m-30) REVERT: C 1097 GLN cc_start: 0.8730 (tp40) cc_final: 0.8438 (tm-30) outliers start: 175 outliers final: 38 residues processed: 813 average time/residue: 0.1703 time to fit residues: 217.3563 Evaluate side-chains 393 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 342 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 0.0970 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 599 GLN A 792 GLN A 812 ASN A 839 ASN A1097 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 ASN A1201 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 670 HIS B 792 GLN B 839 ASN B1023 GLN B1084 GLN B1097 GLN C 111 GLN C 599 GLN C 812 ASN C 839 ASN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 ASN C1201 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.116630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.094966 restraints weight = 221384.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096127 restraints weight = 132654.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.097200 restraints weight = 90789.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097249 restraints weight = 84873.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.097903 restraints weight = 70544.372| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27065 Z= 0.214 Angle : 1.078 16.031 36821 Z= 0.556 Chirality : 0.059 0.330 4131 Planarity : 0.007 0.115 4750 Dihedral : 8.570 55.321 3711 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.27 % Favored : 87.25 % Rotamer: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.74 % Twisted Proline : 0.00 % Twisted General : 1.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.13), residues: 3390 helix: -1.57 (0.16), residues: 699 sheet: -0.52 (0.22), residues: 556 loop : -2.83 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 335 TYR 0.041 0.003 TYR B 438 PHE 0.044 0.002 PHE A 341 TRP 0.017 0.002 TRP C 253 HIS 0.007 0.002 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00452 (27025) covalent geometry : angle 1.07430 (36749) SS BOND : bond 0.00550 ( 36) SS BOND : angle 2.30637 ( 72) hydrogen bonds : bond 0.05126 ( 841) hydrogen bonds : angle 6.94798 ( 2241) Misc. bond : bond 0.00254 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 484 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8377 (m) cc_final: 0.7843 (p) REVERT: A 171 LEU cc_start: 0.8709 (tp) cc_final: 0.8364 (tp) REVERT: A 231 TYR cc_start: 0.7028 (m-80) cc_final: 0.6456 (m-80) REVERT: A 338 ASP cc_start: 0.5652 (p0) cc_final: 0.5365 (p0) REVERT: A 786 PHE cc_start: 0.7837 (m-80) cc_final: 0.7615 (m-10) REVERT: A 819 GLN cc_start: 0.8419 (mt0) cc_final: 0.8141 (tp40) REVERT: A 848 ASN cc_start: 0.8496 (p0) cc_final: 0.8216 (p0) REVERT: A 943 MET cc_start: 0.7658 (ttp) cc_final: 0.6900 (tpp) REVERT: A 1121 THR cc_start: 0.7763 (t) cc_final: 0.7278 (m) REVERT: A 1137 MET cc_start: 0.7421 (mmm) cc_final: 0.7189 (tpt) REVERT: B 49 ASP cc_start: 0.8382 (t0) cc_final: 0.7989 (m-30) REVERT: B 58 TYR cc_start: 0.6478 (t80) cc_final: 0.4520 (t80) REVERT: B 84 MET cc_start: 0.8901 (ttp) cc_final: 0.8528 (ttm) REVERT: B 452 MET cc_start: 0.1431 (mtp) cc_final: 0.1148 (mtp) REVERT: B 569 MET cc_start: 0.3604 (pmm) cc_final: 0.3072 (pmm) REVERT: B 815 GLN cc_start: 0.7799 (mp10) cc_final: 0.7550 (mm110) REVERT: B 827 PHE cc_start: 0.6251 (m-80) cc_final: 0.5898 (m-80) REVERT: B 830 LYS cc_start: 0.8581 (mttt) cc_final: 0.7997 (ptpt) REVERT: B 848 ASN cc_start: 0.8250 (t0) cc_final: 0.8006 (t0) REVERT: B 993 ASN cc_start: 0.7814 (m-40) cc_final: 0.6695 (p0) REVERT: B 1068 ASP cc_start: 0.7802 (m-30) cc_final: 0.7602 (m-30) REVERT: B 1071 ILE cc_start: 0.8469 (mm) cc_final: 0.7940 (mm) REVERT: C 183 PHE cc_start: 0.7845 (p90) cc_final: 0.7427 (p90) REVERT: C 234 LEU cc_start: 0.7092 (mt) cc_final: 0.6696 (mt) REVERT: C 655 VAL cc_start: 0.7313 (t) cc_final: 0.6853 (m) REVERT: C 906 MET cc_start: 0.7125 (mmm) cc_final: 0.6831 (mmm) REVERT: C 938 LEU cc_start: 0.8880 (tt) cc_final: 0.8248 (tt) REVERT: C 943 MET cc_start: 0.6970 (ttp) cc_final: 0.6541 (ttp) REVERT: C 960 TRP cc_start: 0.5952 (t-100) cc_final: 0.5529 (t60) REVERT: C 1044 PHE cc_start: 0.6855 (t80) cc_final: 0.6572 (t80) REVERT: C 1064 ASP cc_start: 0.8414 (m-30) cc_final: 0.7833 (m-30) outliers start: 7 outliers final: 2 residues processed: 489 average time/residue: 0.1619 time to fit residues: 126.7793 Evaluate side-chains 315 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 169 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN A 348 HIS ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 GLN A1027 ASN A1085 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN B 576 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1132 ASN C 111 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN C1201 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.115074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.092494 restraints weight = 198762.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094644 restraints weight = 120989.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095585 restraints weight = 71388.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095856 restraints weight = 69498.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.095927 restraints weight = 58260.291| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27065 Z= 0.199 Angle : 1.010 14.489 36821 Z= 0.519 Chirality : 0.056 0.315 4131 Planarity : 0.006 0.104 4750 Dihedral : 7.958 56.885 3711 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.28 % Favored : 86.31 % Rotamer: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.68 % Twisted General : 0.77 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.13), residues: 3390 helix: -0.66 (0.18), residues: 673 sheet: -0.57 (0.21), residues: 589 loop : -2.74 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 691 TYR 0.038 0.002 TYR C1186 PHE 0.033 0.002 PHE A 895 TRP 0.012 0.002 TRP A 310 HIS 0.011 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00424 (27025) covalent geometry : angle 1.00568 (36749) SS BOND : bond 0.00435 ( 36) SS BOND : angle 2.38848 ( 72) hydrogen bonds : bond 0.04753 ( 841) hydrogen bonds : angle 6.58950 ( 2241) Misc. bond : bond 0.00179 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8467 (m) cc_final: 0.7967 (p) REVERT: A 231 TYR cc_start: 0.7144 (m-80) cc_final: 0.6589 (m-80) REVERT: A 384 ASP cc_start: 0.7823 (p0) cc_final: 0.7608 (p0) REVERT: A 569 MET cc_start: -0.0993 (ttt) cc_final: -0.1294 (ptm) REVERT: A 829 SER cc_start: 0.8287 (m) cc_final: 0.7473 (m) REVERT: A 848 ASN cc_start: 0.8659 (p0) cc_final: 0.8410 (p0) REVERT: A 927 GLN cc_start: 0.7280 (pp30) cc_final: 0.6723 (pp30) REVERT: A 943 MET cc_start: 0.7444 (ttp) cc_final: 0.6961 (tpp) REVERT: A 1137 MET cc_start: 0.7585 (mmm) cc_final: 0.7302 (tpt) REVERT: B 49 ASP cc_start: 0.8516 (t0) cc_final: 0.8214 (m-30) REVERT: B 215 SER cc_start: 0.8085 (m) cc_final: 0.7820 (t) REVERT: B 452 MET cc_start: 0.1479 (mtp) cc_final: 0.1130 (mtm) REVERT: B 499 TYR cc_start: 0.7925 (p90) cc_final: 0.7702 (p90) REVERT: B 569 MET cc_start: 0.3981 (pmm) cc_final: 0.3619 (pmm) REVERT: C 234 LEU cc_start: 0.7161 (mt) cc_final: 0.6916 (tp) REVERT: C 271 VAL cc_start: 0.7441 (t) cc_final: 0.7226 (t) REVERT: C 283 THR cc_start: 0.7732 (m) cc_final: 0.7230 (m) REVERT: C 655 VAL cc_start: 0.7543 (t) cc_final: 0.7020 (m) REVERT: C 849 LEU cc_start: 0.9097 (tt) cc_final: 0.8895 (tp) REVERT: C 892 ASP cc_start: 0.8114 (m-30) cc_final: 0.7907 (m-30) REVERT: C 992 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7235 (mp0) REVERT: C 1036 LEU cc_start: 0.9323 (mt) cc_final: 0.8833 (mm) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.1564 time to fit residues: 109.1055 Evaluate side-chains 287 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 13 optimal weight: 30.0000 chunk 188 optimal weight: 6.9990 chunk 333 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 279 optimal weight: 30.0000 chunk 257 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 295 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 220 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 765 ASN A 800 GLN A1097 GLN A1132 ASN B 628 GLN B 836 HIS B1084 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN C1201 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.092539 restraints weight = 216116.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.093794 restraints weight = 125693.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.095159 restraints weight = 84983.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094828 restraints weight = 64743.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095188 restraints weight = 65621.558| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27065 Z= 0.190 Angle : 0.979 13.952 36821 Z= 0.500 Chirality : 0.054 0.296 4131 Planarity : 0.006 0.106 4750 Dihedral : 7.651 54.241 3711 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.93 % Favored : 86.78 % Rotamer: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.13), residues: 3390 helix: -0.50 (0.19), residues: 688 sheet: -0.44 (0.21), residues: 561 loop : -2.68 (0.12), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1179 TYR 0.032 0.002 TYR B 438 PHE 0.059 0.002 PHE B 764 TRP 0.017 0.001 TRP C1184 HIS 0.009 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00402 (27025) covalent geometry : angle 0.97566 (36749) SS BOND : bond 0.00394 ( 36) SS BOND : angle 2.12704 ( 72) hydrogen bonds : bond 0.04552 ( 841) hydrogen bonds : angle 6.44049 ( 2241) Misc. bond : bond 0.00281 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 404 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8473 (m) cc_final: 0.7937 (p) REVERT: A 677 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 848 ASN cc_start: 0.8752 (p0) cc_final: 0.8428 (p0) REVERT: A 927 GLN cc_start: 0.7190 (pp30) cc_final: 0.6416 (pp30) REVERT: A 943 MET cc_start: 0.7327 (ttp) cc_final: 0.7088 (ttp) REVERT: A 1100 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8727 (ptpp) REVERT: B 49 ASP cc_start: 0.8593 (t0) cc_final: 0.8058 (m-30) REVERT: B 215 SER cc_start: 0.7593 (m) cc_final: 0.7303 (t) REVERT: B 452 MET cc_start: 0.1268 (mtp) cc_final: 0.0905 (mtm) REVERT: B 499 TYR cc_start: 0.7827 (p90) cc_final: 0.7605 (p90) REVERT: B 569 MET cc_start: 0.4094 (pmm) cc_final: 0.3309 (pmm) REVERT: B 830 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8275 (pttp) REVERT: B 960 TRP cc_start: 0.7205 (t-100) cc_final: 0.6791 (t60) REVERT: B 1075 LEU cc_start: 0.8703 (tt) cc_final: 0.8002 (tp) REVERT: B 1172 PHE cc_start: 0.6825 (m-80) cc_final: 0.6462 (m-80) REVERT: C 271 VAL cc_start: 0.7474 (t) cc_final: 0.7237 (t) REVERT: C 1036 LEU cc_start: 0.9413 (mt) cc_final: 0.9041 (mm) outliers start: 2 outliers final: 0 residues processed: 406 average time/residue: 0.1558 time to fit residues: 102.6752 Evaluate side-chains 272 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 238 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 339 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 273 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 332 optimal weight: 3.9990 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN A1009 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN A1163 ASN B 114 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN B 681 HIS B 765 ASN B 766 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN B1084 GLN B1201 ASN C 769 GLN ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.108428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086199 restraints weight = 207977.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086694 restraints weight = 132062.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087539 restraints weight = 92994.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087534 restraints weight = 89706.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.088114 restraints weight = 73835.518| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 27065 Z= 0.298 Angle : 1.092 13.760 36821 Z= 0.562 Chirality : 0.058 0.335 4131 Planarity : 0.007 0.107 4750 Dihedral : 8.014 56.743 3711 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.73 % Favored : 84.92 % Rotamer: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.13), residues: 3390 helix: -0.66 (0.18), residues: 673 sheet: -1.14 (0.22), residues: 557 loop : -2.69 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 626 TYR 0.056 0.003 TYR B 609 PHE 0.059 0.003 PHE B 764 TRP 0.031 0.003 TRP B 44 HIS 0.012 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00648 (27025) covalent geometry : angle 1.08916 (36749) SS BOND : bond 0.00525 ( 36) SS BOND : angle 1.97905 ( 72) hydrogen bonds : bond 0.05258 ( 841) hydrogen bonds : angle 6.78374 ( 2241) Misc. bond : bond 0.00271 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8533 (m) cc_final: 0.8109 (p) REVERT: A 161 MET cc_start: 0.7669 (tpp) cc_final: 0.7349 (tpt) REVERT: A 344 LEU cc_start: 0.8320 (pp) cc_final: 0.7978 (mp) REVERT: A 351 TYR cc_start: 0.7855 (m-80) cc_final: 0.7585 (m-80) REVERT: A 361 TYR cc_start: 0.8808 (m-80) cc_final: 0.8583 (m-80) REVERT: A 384 ASP cc_start: 0.7956 (p0) cc_final: 0.7656 (p0) REVERT: A 841 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7930 (ptp90) REVERT: A 848 ASN cc_start: 0.8849 (p0) cc_final: 0.8593 (p0) REVERT: A 952 LEU cc_start: 0.8890 (mp) cc_final: 0.8542 (tt) REVERT: A 987 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6678 (mm-40) REVERT: A 1127 VAL cc_start: 0.9018 (t) cc_final: 0.8768 (p) REVERT: A 1137 MET cc_start: 0.7924 (mmm) cc_final: 0.7684 (tpt) REVERT: B 215 SER cc_start: 0.7644 (m) cc_final: 0.7423 (t) REVERT: B 343 ASP cc_start: 0.7126 (m-30) cc_final: 0.6697 (m-30) REVERT: B 382 GLU cc_start: 0.8260 (tt0) cc_final: 0.7776 (tm-30) REVERT: B 448 TYR cc_start: 0.3143 (t80) cc_final: 0.2573 (t80) REVERT: B 569 MET cc_start: 0.4073 (pmm) cc_final: 0.3334 (pmm) REVERT: B 830 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8295 (pttm) REVERT: B 833 GLN cc_start: 0.8896 (mt0) cc_final: 0.8691 (mt0) REVERT: B 906 MET cc_start: 0.6636 (ppp) cc_final: 0.6325 (ppp) REVERT: B 951 LEU cc_start: 0.9029 (tp) cc_final: 0.8828 (tt) REVERT: B 976 ILE cc_start: 0.9162 (mm) cc_final: 0.8881 (tt) REVERT: B 1075 LEU cc_start: 0.9044 (tt) cc_final: 0.8816 (tp) REVERT: B 1076 THR cc_start: 0.7692 (t) cc_final: 0.7246 (t) REVERT: B 1079 ASN cc_start: 0.8491 (m-40) cc_final: 0.8206 (m-40) REVERT: B 1086 LEU cc_start: 0.8861 (mt) cc_final: 0.7712 (mt) REVERT: B 1090 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6843 (mp0) REVERT: B 1172 PHE cc_start: 0.7113 (m-80) cc_final: 0.6720 (m-80) REVERT: B 1190 SER cc_start: 0.8455 (m) cc_final: 0.8252 (p) REVERT: C 271 VAL cc_start: 0.8043 (t) cc_final: 0.7832 (t) REVERT: C 351 TYR cc_start: 0.7763 (m-10) cc_final: 0.7468 (m-10) REVERT: C 696 MET cc_start: 0.6888 (mmp) cc_final: 0.6600 (mmm) REVERT: C 849 LEU cc_start: 0.9119 (tt) cc_final: 0.8897 (tp) REVERT: C 928 TYR cc_start: 0.5729 (m-80) cc_final: 0.5270 (m-10) REVERT: C 1013 THR cc_start: 0.8337 (p) cc_final: 0.8131 (p) REVERT: C 1064 ASP cc_start: 0.8509 (m-30) cc_final: 0.8081 (m-30) outliers start: 1 outliers final: 1 residues processed: 343 average time/residue: 0.1650 time to fit residues: 91.6682 Evaluate side-chains 241 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 236 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 165 optimal weight: 40.0000 chunk 313 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 765 ASN A1009 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1201 ASN C 486 HIS C 670 HIS C 766 HIS C 769 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.108687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.086632 restraints weight = 246381.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.087202 restraints weight = 142307.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088729 restraints weight = 104277.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.088234 restraints weight = 81399.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.088656 restraints weight = 86384.541| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 27065 Z= 0.242 Angle : 1.013 12.745 36821 Z= 0.520 Chirality : 0.056 0.305 4131 Planarity : 0.006 0.105 4750 Dihedral : 7.719 50.526 3711 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.40 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.13), residues: 3390 helix: -0.58 (0.18), residues: 694 sheet: -0.80 (0.22), residues: 542 loop : -2.81 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 181 TYR 0.061 0.002 TYR B 648 PHE 0.058 0.002 PHE B 764 TRP 0.026 0.002 TRP B 44 HIS 0.020 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00527 (27025) covalent geometry : angle 1.00661 (36749) SS BOND : bond 0.00509 ( 36) SS BOND : angle 2.79665 ( 72) hydrogen bonds : bond 0.04848 ( 841) hydrogen bonds : angle 6.61915 ( 2241) Misc. bond : bond 0.00151 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8503 (m) cc_final: 0.8092 (p) REVERT: A 161 MET cc_start: 0.7923 (tpp) cc_final: 0.7690 (tpt) REVERT: A 351 TYR cc_start: 0.7734 (m-80) cc_final: 0.7504 (m-80) REVERT: A 841 ARG cc_start: 0.8312 (ptp90) cc_final: 0.8080 (ptp90) REVERT: A 848 ASN cc_start: 0.8707 (p0) cc_final: 0.8491 (p0) REVERT: A 952 LEU cc_start: 0.8817 (mp) cc_final: 0.8446 (tt) REVERT: A 1137 MET cc_start: 0.7975 (mmm) cc_final: 0.7711 (tpt) REVERT: B 215 SER cc_start: 0.7595 (m) cc_final: 0.7393 (t) REVERT: B 382 GLU cc_start: 0.8338 (tt0) cc_final: 0.7829 (tm-30) REVERT: B 448 TYR cc_start: 0.3566 (t80) cc_final: 0.3197 (t80) REVERT: B 452 MET cc_start: 0.1680 (mtp) cc_final: 0.1452 (mtm) REVERT: B 830 LYS cc_start: 0.9009 (ptpt) cc_final: 0.8338 (pttm) REVERT: B 906 MET cc_start: 0.6593 (ppp) cc_final: 0.6294 (ppp) REVERT: B 1086 LEU cc_start: 0.8844 (mt) cc_final: 0.7725 (mt) REVERT: B 1090 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6970 (mp0) REVERT: B 1172 PHE cc_start: 0.7040 (m-80) cc_final: 0.6564 (m-80) REVERT: C 271 VAL cc_start: 0.7939 (t) cc_final: 0.7714 (t) REVERT: C 283 THR cc_start: 0.8113 (m) cc_final: 0.7898 (m) REVERT: C 563 MET cc_start: 0.2292 (mmt) cc_final: 0.1606 (mmt) REVERT: C 827 PHE cc_start: 0.8360 (m-80) cc_final: 0.8003 (m-10) REVERT: C 928 TYR cc_start: 0.5891 (m-80) cc_final: 0.5418 (m-10) REVERT: C 1015 THR cc_start: 0.8656 (p) cc_final: 0.8412 (t) REVERT: C 1042 ASN cc_start: 0.7619 (p0) cc_final: 0.7411 (p0) REVERT: C 1064 ASP cc_start: 0.8457 (m-30) cc_final: 0.8045 (m-30) REVERT: C 1179 ARG cc_start: 0.7009 (tpt170) cc_final: 0.6328 (tpp-160) REVERT: C 1187 THR cc_start: 0.7751 (p) cc_final: 0.7294 (p) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1540 time to fit residues: 85.6641 Evaluate side-chains 241 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 163 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 11 optimal weight: 40.0000 chunk 171 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 314 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1084 GLN B1201 ASN C 785 ASN C 833 GLN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.110268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088135 restraints weight = 231865.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.089542 restraints weight = 132752.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090743 restraints weight = 89333.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090598 restraints weight = 70533.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.091134 restraints weight = 63769.855| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27065 Z= 0.186 Angle : 0.972 15.580 36821 Z= 0.494 Chirality : 0.054 0.286 4131 Planarity : 0.006 0.102 4750 Dihedral : 7.414 47.176 3711 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.17 % Favored : 85.54 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.13), residues: 3390 helix: -0.33 (0.19), residues: 687 sheet: -0.93 (0.21), residues: 580 loop : -2.74 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 887 TYR 0.051 0.002 TYR A1186 PHE 0.039 0.002 PHE B 764 TRP 0.019 0.002 TRP A1184 HIS 0.007 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00398 (27025) covalent geometry : angle 0.96733 (36749) SS BOND : bond 0.00406 ( 36) SS BOND : angle 2.41306 ( 72) hydrogen bonds : bond 0.04503 ( 841) hydrogen bonds : angle 6.44990 ( 2241) Misc. bond : bond 0.00139 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8438 (m) cc_final: 0.8045 (p) REVERT: A 161 MET cc_start: 0.7878 (tpp) cc_final: 0.7676 (tpt) REVERT: A 251 LEU cc_start: 0.6987 (pt) cc_final: 0.6554 (tp) REVERT: A 343 ASP cc_start: 0.7952 (m-30) cc_final: 0.7270 (m-30) REVERT: A 351 TYR cc_start: 0.7717 (m-80) cc_final: 0.7464 (m-80) REVERT: A 361 TYR cc_start: 0.8549 (m-10) cc_final: 0.8140 (m-10) REVERT: A 384 ASP cc_start: 0.7719 (p0) cc_final: 0.6690 (t70) REVERT: A 848 ASN cc_start: 0.8657 (p0) cc_final: 0.8422 (p0) REVERT: A 938 LEU cc_start: 0.9127 (tt) cc_final: 0.8911 (tt) REVERT: A 943 MET cc_start: 0.7083 (tpt) cc_final: 0.6753 (tpt) REVERT: A 952 LEU cc_start: 0.8786 (mp) cc_final: 0.8457 (tt) REVERT: B 382 GLU cc_start: 0.8526 (tt0) cc_final: 0.7988 (tm-30) REVERT: B 448 TYR cc_start: 0.3739 (t80) cc_final: 0.3348 (t80) REVERT: B 569 MET cc_start: 0.3281 (pmm) cc_final: 0.2783 (pmm) REVERT: B 906 MET cc_start: 0.6645 (ppp) cc_final: 0.6373 (ppp) REVERT: B 1075 LEU cc_start: 0.8961 (tp) cc_final: 0.8629 (tp) REVERT: B 1086 LEU cc_start: 0.8738 (mt) cc_final: 0.7316 (mt) REVERT: B 1172 PHE cc_start: 0.7165 (m-80) cc_final: 0.6962 (m-80) REVERT: B 1185 SER cc_start: 0.8804 (m) cc_final: 0.8409 (p) REVERT: C 271 VAL cc_start: 0.7820 (t) cc_final: 0.7579 (t) REVERT: C 283 THR cc_start: 0.8054 (m) cc_final: 0.7827 (m) REVERT: C 563 MET cc_start: 0.2098 (mmt) cc_final: 0.1484 (mmt) REVERT: C 827 PHE cc_start: 0.8166 (m-80) cc_final: 0.7793 (m-10) REVERT: C 928 TYR cc_start: 0.5252 (m-80) cc_final: 0.4876 (m-10) REVERT: C 1064 ASP cc_start: 0.8395 (m-30) cc_final: 0.8030 (m-30) REVERT: C 1179 ARG cc_start: 0.6873 (tpt170) cc_final: 0.5927 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1536 time to fit residues: 84.9926 Evaluate side-chains 237 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 89 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 336 optimal weight: 20.0000 chunk 51 optimal weight: 40.0000 chunk 304 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 0.0060 chunk 219 optimal weight: 0.3980 chunk 318 optimal weight: 3.9990 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN A1132 ASN A1201 ASN B 218 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1201 ASN C 627 GLN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.110446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088128 restraints weight = 257841.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.089622 restraints weight = 147734.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090787 restraints weight = 100710.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.090313 restraints weight = 83573.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090992 restraints weight = 79089.031| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27065 Z= 0.181 Angle : 0.964 15.304 36821 Z= 0.490 Chirality : 0.054 0.293 4131 Planarity : 0.006 0.102 4750 Dihedral : 7.266 43.663 3711 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.87 % Favored : 85.80 % Rotamer: Outliers : 0.07 % Allowed : 0.82 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.68 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.14), residues: 3390 helix: -0.23 (0.19), residues: 684 sheet: -0.77 (0.22), residues: 574 loop : -2.73 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1057 TYR 0.053 0.002 TYR A1186 PHE 0.036 0.002 PHE B 764 TRP 0.017 0.002 TRP C 960 HIS 0.006 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00387 (27025) covalent geometry : angle 0.96026 (36749) SS BOND : bond 0.00406 ( 36) SS BOND : angle 2.20252 ( 72) hydrogen bonds : bond 0.04401 ( 841) hydrogen bonds : angle 6.43502 ( 2241) Misc. bond : bond 0.00120 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8446 (m) cc_final: 0.8095 (p) REVERT: A 161 MET cc_start: 0.7937 (tpp) cc_final: 0.7707 (tpt) REVERT: A 251 LEU cc_start: 0.6992 (pt) cc_final: 0.6596 (tp) REVERT: A 343 ASP cc_start: 0.8075 (m-30) cc_final: 0.7609 (m-30) REVERT: A 351 TYR cc_start: 0.7740 (m-80) cc_final: 0.7440 (m-80) REVERT: A 384 ASP cc_start: 0.7910 (p0) cc_final: 0.6924 (t70) REVERT: A 563 MET cc_start: 0.6892 (mmm) cc_final: 0.4019 (ptt) REVERT: A 642 TYR cc_start: 0.5160 (m-10) cc_final: 0.3384 (m-10) REVERT: A 943 MET cc_start: 0.7132 (tpt) cc_final: 0.6822 (tpt) REVERT: A 952 LEU cc_start: 0.8837 (mp) cc_final: 0.8502 (tt) REVERT: A 1127 VAL cc_start: 0.8999 (t) cc_final: 0.8715 (p) REVERT: B 569 MET cc_start: 0.3103 (pmm) cc_final: 0.2669 (pmm) REVERT: B 1172 PHE cc_start: 0.7265 (m-80) cc_final: 0.6905 (m-80) REVERT: B 1185 SER cc_start: 0.8856 (m) cc_final: 0.8247 (p) REVERT: C 271 VAL cc_start: 0.7695 (t) cc_final: 0.7459 (t) REVERT: C 563 MET cc_start: 0.2787 (mmt) cc_final: 0.2190 (mmt) REVERT: C 827 PHE cc_start: 0.8144 (m-80) cc_final: 0.7744 (m-10) REVERT: C 928 TYR cc_start: 0.5302 (m-80) cc_final: 0.4845 (m-10) REVERT: C 1064 ASP cc_start: 0.8475 (m-30) cc_final: 0.8127 (m-30) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.1600 time to fit residues: 88.4653 Evaluate side-chains 229 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 316 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 222 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1023 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1084 GLN B1201 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN C 800 GLN C 833 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.107484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.086244 restraints weight = 221658.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086590 restraints weight = 140133.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087612 restraints weight = 107930.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.087209 restraints weight = 89063.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.087749 restraints weight = 83062.438| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 27065 Z= 0.253 Angle : 1.025 14.000 36821 Z= 0.524 Chirality : 0.056 0.363 4131 Planarity : 0.006 0.101 4750 Dihedral : 7.520 45.107 3711 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.03 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.14), residues: 3390 helix: -0.25 (0.19), residues: 671 sheet: -1.23 (0.21), residues: 600 loop : -2.76 (0.12), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1179 TYR 0.046 0.003 TYR C 648 PHE 0.060 0.003 PHE B 778 TRP 0.031 0.003 TRP A1184 HIS 0.007 0.002 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00548 (27025) covalent geometry : angle 1.02166 (36749) SS BOND : bond 0.00467 ( 36) SS BOND : angle 2.19689 ( 72) hydrogen bonds : bond 0.04720 ( 841) hydrogen bonds : angle 6.59371 ( 2241) Misc. bond : bond 0.00205 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8508 (m) cc_final: 0.8206 (p) REVERT: A 351 TYR cc_start: 0.7905 (m-80) cc_final: 0.7564 (m-80) REVERT: A 563 MET cc_start: 0.6880 (mmm) cc_final: 0.4276 (ptt) REVERT: A 952 LEU cc_start: 0.8863 (mp) cc_final: 0.8601 (tt) REVERT: B 569 MET cc_start: 0.3074 (pmm) cc_final: 0.2703 (pmm) REVERT: B 829 SER cc_start: 0.8984 (m) cc_final: 0.8550 (p) REVERT: B 932 TYR cc_start: 0.6408 (p90) cc_final: 0.6188 (p90) REVERT: B 1185 SER cc_start: 0.8963 (m) cc_final: 0.8756 (p) REVERT: C 183 PHE cc_start: 0.8282 (p90) cc_final: 0.7972 (p90) REVERT: C 228 PHE cc_start: 0.8840 (t80) cc_final: 0.8559 (t80) REVERT: C 271 VAL cc_start: 0.7914 (t) cc_final: 0.7625 (t) REVERT: C 286 VAL cc_start: 0.7580 (t) cc_final: 0.6885 (t) REVERT: C 563 MET cc_start: 0.2844 (mmt) cc_final: 0.2237 (mmt) REVERT: C 696 MET cc_start: 0.7573 (tpt) cc_final: 0.7268 (tpt) REVERT: C 928 TYR cc_start: 0.5695 (m-80) cc_final: 0.5307 (m-10) REVERT: C 943 MET cc_start: 0.8405 (tpt) cc_final: 0.8161 (tpp) REVERT: C 1064 ASP cc_start: 0.8437 (m-30) cc_final: 0.8114 (m-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.1517 time to fit residues: 78.0656 Evaluate side-chains 226 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 42 optimal weight: 40.0000 chunk 335 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 238 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 overall best weight: 2.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1146 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B1079 ASN B1084 GLN C 277 ASN C 833 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.110065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088440 restraints weight = 211820.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089226 restraints weight = 132512.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089673 restraints weight = 98516.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.089970 restraints weight = 85709.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.090401 restraints weight = 71971.964| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27065 Z= 0.176 Angle : 0.961 13.274 36821 Z= 0.488 Chirality : 0.054 0.310 4131 Planarity : 0.006 0.102 4750 Dihedral : 7.213 40.771 3711 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.93 % Favored : 85.77 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.14), residues: 3390 helix: -0.11 (0.19), residues: 672 sheet: -1.10 (0.23), residues: 529 loop : -2.68 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1179 TYR 0.049 0.002 TYR A1186 PHE 0.036 0.002 PHE A1001 TRP 0.016 0.001 TRP C 960 HIS 0.010 0.001 HIS A1146 Details of bonding type rmsd covalent geometry : bond 0.00375 (27025) covalent geometry : angle 0.95710 (36749) SS BOND : bond 0.00375 ( 36) SS BOND : angle 2.13455 ( 72) hydrogen bonds : bond 0.04468 ( 841) hydrogen bonds : angle 6.39848 ( 2241) Misc. bond : bond 0.00246 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8474 (m) cc_final: 0.8203 (p) REVERT: A 218 ASN cc_start: 0.8151 (t0) cc_final: 0.7945 (t0) REVERT: A 251 LEU cc_start: 0.6922 (pt) cc_final: 0.6527 (tp) REVERT: A 361 TYR cc_start: 0.8641 (m-10) cc_final: 0.8360 (m-10) REVERT: A 384 ASP cc_start: 0.7833 (p0) cc_final: 0.6988 (t70) REVERT: A 563 MET cc_start: 0.6996 (mmm) cc_final: 0.4498 (ptt) REVERT: A 848 ASN cc_start: 0.8648 (p0) cc_final: 0.8430 (p0) REVERT: A 952 LEU cc_start: 0.8869 (mp) cc_final: 0.8589 (tt) REVERT: A 985 ILE cc_start: 0.8844 (mt) cc_final: 0.8507 (mt) REVERT: A 1090 GLU cc_start: 0.8814 (mp0) cc_final: 0.7678 (mp0) REVERT: A 1127 VAL cc_start: 0.8997 (t) cc_final: 0.8681 (p) REVERT: B 569 MET cc_start: 0.3332 (pmm) cc_final: 0.3030 (pmm) REVERT: B 829 SER cc_start: 0.8855 (m) cc_final: 0.8350 (p) REVERT: B 906 MET cc_start: 0.5869 (ppp) cc_final: 0.5114 (ppp) REVERT: C 183 PHE cc_start: 0.8232 (p90) cc_final: 0.8000 (p90) REVERT: C 228 PHE cc_start: 0.8776 (t80) cc_final: 0.8503 (t80) REVERT: C 271 VAL cc_start: 0.7810 (t) cc_final: 0.7558 (t) REVERT: C 361 TYR cc_start: 0.8486 (m-80) cc_final: 0.8282 (m-80) REVERT: C 563 MET cc_start: 0.2687 (mmt) cc_final: 0.2084 (mmt) REVERT: C 633 ASP cc_start: 0.7952 (t70) cc_final: 0.7617 (p0) REVERT: C 696 MET cc_start: 0.7393 (tpt) cc_final: 0.7152 (tpt) REVERT: C 827 PHE cc_start: 0.8239 (m-80) cc_final: 0.7903 (m-10) REVERT: C 928 TYR cc_start: 0.5120 (m-80) cc_final: 0.4688 (m-10) REVERT: C 1064 ASP cc_start: 0.8505 (m-30) cc_final: 0.8158 (m-30) REVERT: C 1179 ARG cc_start: 0.6129 (mmt180) cc_final: 0.5846 (mmt180) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1484 time to fit residues: 79.4510 Evaluate side-chains 236 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 114 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 142 optimal weight: 0.0020 chunk 90 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1163 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 ASN B 993 ASN B1079 ASN B1084 GLN B1201 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.088759 restraints weight = 258814.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.090315 restraints weight = 151351.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.091102 restraints weight = 104477.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.091376 restraints weight = 77091.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.091886 restraints weight = 70208.516| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.8005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27065 Z= 0.178 Angle : 0.952 15.156 36821 Z= 0.483 Chirality : 0.054 0.309 4131 Planarity : 0.006 0.103 4750 Dihedral : 7.070 40.189 3711 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.34 % Favored : 85.36 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.14), residues: 3390 helix: -0.12 (0.19), residues: 665 sheet: -1.01 (0.23), residues: 521 loop : -2.66 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1179 TYR 0.041 0.002 TYR A1186 PHE 0.035 0.002 PHE A1001 TRP 0.015 0.001 TRP A1184 HIS 0.006 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00382 (27025) covalent geometry : angle 0.94922 (36749) SS BOND : bond 0.00343 ( 36) SS BOND : angle 1.99050 ( 72) hydrogen bonds : bond 0.04388 ( 841) hydrogen bonds : angle 6.35644 ( 2241) Misc. bond : bond 0.00228 ( 4) =============================================================================== Job complete usr+sys time: 4626.19 seconds wall clock time: 80 minutes 56.89 seconds (4856.89 seconds total)