Starting phenix.real_space_refine on Fri Sep 19 12:23:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x5c_6706/09_2025/5x5c_6706.map" } resolution = 4.1 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= 0.013 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 16797 2.51 5 N 4371 2.21 5 O 5097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s 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: 26418 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 5 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 5 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: 8994 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': 41, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1049} 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': 41, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1049} 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: 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': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} 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': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} 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 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: 11.54, per 1000 atoms: 0.44 Number of scatterers: 26418 At special positions: 0 Unit cell: (152.1, 163.8, 180.7, 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 5097 8.00 N 4371 7.00 C 16797 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=2.71 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=2.02 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=2.56 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=2.01 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=2.74 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=2.03 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: 2.51 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 715.3 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: 1.09 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: 3.677A 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 removed outlier: 4.206A pdb=" N SER A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' 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: 3.879A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.043A 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: 3.925A 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: 4.472A 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: 3.973A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.717A 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: 3.677A 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: 4.196A 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: 3.613A 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: 3.639A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.973A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.717A 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 1062 through 1107 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: 3.883A 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: 3.825A 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: 3.613A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.879A 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: 5.043A 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: 4.471A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.972A 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: 4.060A 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: 6.250A 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: 6.149A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.338A 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: 7.160A 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: 6.469A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.822A 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: 4.304A 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: 3.858A 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: 5.878A 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: 6.788A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.577A 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: 6.071A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.321A 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: 4.597A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.465A 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: 4.070A 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: 6.149A 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: 7.161A 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: 6.510A 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: 6.821A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.440A 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: 5.878A 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 405 removed outlier: 3.894A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.788A 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 408 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 514 through 515 removed outlier: 3.697A pdb=" N VAL B 514 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 505 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.071A 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: 4.557A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.717A 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: 4.098A 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: 7.160A 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: 6.510A 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: 6.822A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.817A 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: 3.858A 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: 5.878A 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: 6.788A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.577A 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: 4.321A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.465A 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 834 hydrogen bonds defined for protein. 2226 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: 6.12 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 22865 1.53 - 1.86: 4156 1.86 - 2.20: 0 2.20 - 2.54: 0 2.54 - 2.88: 1 Bond restraints: 27022 Sorted by residual: bond pdb=" C LEU A 588 " pdb=" N LYS A 595 " ideal model delta sigma weight residual 1.332 2.879 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C TYR B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.12e+01 bond pdb=" C TYR A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.12e+01 bond pdb=" C TYR C 58 " pdb=" N PRO C 59 " ideal model delta sigma weight residual 1.333 1.408 -0.075 1.17e-02 7.31e+03 4.10e+01 bond pdb=" C GLN A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.332 1.406 -0.074 1.30e-02 5.92e+03 3.27e+01 ... (remaining 27017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.00: 36740 19.00 - 37.99: 6 37.99 - 56.99: 0 56.99 - 75.99: 0 75.99 - 94.99: 1 Bond angle restraints: 36747 Sorted by residual: angle pdb=" O LEU A 588 " pdb=" C LEU A 588 " pdb=" N LYS A 595 " ideal model delta sigma weight residual 122.59 27.60 94.99 1.33e+00 5.65e-01 5.10e+03 angle pdb=" N SER B 508 " pdb=" CA SER B 508 " pdb=" C SER B 508 " ideal model delta sigma weight residual 110.35 94.93 15.42 1.36e+00 5.41e-01 1.29e+02 angle pdb=" N TYR B 663 " pdb=" CA TYR B 663 " pdb=" C TYR B 663 " ideal model delta sigma weight residual 111.14 123.25 -12.11 1.08e+00 8.57e-01 1.26e+02 angle pdb=" C SER A1151 " pdb=" N ALA A1152 " pdb=" CA ALA A1152 " ideal model delta sigma weight residual 121.70 140.12 -18.42 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C SER C1151 " pdb=" N ALA C1152 " pdb=" CA ALA C1152 " ideal model delta sigma weight residual 121.70 140.09 -18.39 1.80e+00 3.09e-01 1.04e+02 ... (remaining 36742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15407 26.90 - 53.80: 580 53.80 - 80.69: 70 80.69 - 107.59: 9 107.59 - 134.49: 9 Dihedral angle restraints: 16075 sinusoidal: 6084 harmonic: 9991 Sorted by residual: 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 -45.51 -134.49 0 5.00e+00 4.00e-02 7.23e+02 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 -45.59 -134.41 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 ... (remaining 16072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3413 0.097 - 0.195: 599 0.195 - 0.292: 79 0.292 - 0.390: 29 0.390 - 0.487: 11 Chirality restraints: 4131 Sorted by residual: chirality pdb=" CA ASP B 580 " pdb=" N ASP B 580 " pdb=" C ASP B 580 " pdb=" CB ASP B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 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 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA TYR B 663 " pdb=" N TYR B 663 " pdb=" C TYR B 663 " pdb=" CB TYR B 663 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 4128 not shown) Planarity restraints: 4750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 588 " -0.019 2.00e-02 2.50e+03 2.30e-01 5.29e+02 pdb=" C LEU A 588 " 0.253 2.00e-02 2.50e+03 pdb=" O LEU A 588 " -0.362 2.00e-02 2.50e+03 pdb=" N LYS A 595 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+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 5.23e-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: 1.47 - 2.15: 79 2.15 - 2.84: 9319 2.84 - 3.53: 36037 3.53 - 4.21: 66066 4.21 - 4.90: 108630 Nonbonded interactions: 220131 Sorted by model distance: nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 1.466 3.040 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 1.466 3.040 nonbonded pdb=" OH TYR A 58 " pdb=" O GLY A 331 " model vdw 1.466 3.040 nonbonded pdb=" N GLN C 78 " pdb=" OD2 ASP C 338 " model vdw 1.474 3.120 nonbonded pdb=" CG2 THR A 68 " pdb=" O LEU A 325 " model vdw 1.485 3.460 ... (remaining 220126 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: 0.04 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 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.320 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.016 1.546 27062 Z= 0.960 Angle : 1.855 94.986 36819 Z= 1.069 Chirality : 0.082 0.487 4131 Planarity : 0.009 0.230 4750 Dihedral : 14.644 134.489 9583 Min Nonbonded Distance : 1.466 Molprobity Statistics. All-atom Clashscore : 30.49 Ramachandran Plot: Outliers : 1.21 % Allowed : 13.22 % Favored : 85.57 % Rotamer: Outliers : 5.82 % Allowed : 7.30 % Favored : 86.88 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.22 % Twisted Proline : 0.00 % Twisted General : 1.75 % 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: -3.80 (0.12), residues: 3390 helix: -2.83 (0.14), residues: 674 sheet: -1.27 (0.21), residues: 579 loop : -2.95 (0.11), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 119 TYR 0.046 0.004 TYR C1171 PHE 0.038 0.004 PHE A1172 TRP 0.032 0.005 TRP A 960 HIS 0.016 0.004 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.01407 (27022) covalent geometry : angle 1.75283 (36747) SS BOND : bond 0.19953 ( 36) SS BOND : angle 13.87294 ( 72) hydrogen bonds : bond 0.16451 ( 834) hydrogen bonds : angle 10.53945 ( 2226) Misc. bond : bond 0.20531 ( 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 851 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 681 time to evaluate : 1.056 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5284 (t80) REVERT: A 564 THR cc_start: 0.2204 (OUTLIER) cc_final: 0.1847 (p) REVERT: A 604 VAL cc_start: 0.5328 (t) cc_final: 0.5102 (m) REVERT: A 607 SER cc_start: 0.8225 (t) cc_final: 0.8014 (p) REVERT: A 757 MET cc_start: 0.8361 (tpt) cc_final: 0.8125 (mmt) REVERT: A 895 PHE cc_start: 0.8873 (m-80) cc_final: 0.8339 (m-80) REVERT: A 943 MET cc_start: 0.7159 (ttp) cc_final: 0.6682 (ttp) REVERT: A 947 TYR cc_start: 0.8308 (m-80) cc_final: 0.7868 (m-80) REVERT: B 352 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 465 SER cc_start: 0.4707 (OUTLIER) cc_final: 0.4173 (t) REVERT: B 493 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3960 (mptt) REVERT: B 511 ARG cc_start: 0.0923 (OUTLIER) cc_final: 0.0214 (mtp180) REVERT: B 563 MET cc_start: 0.3867 (tpp) cc_final: 0.3486 (ttp) REVERT: B 565 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4992 (tp30) REVERT: B 725 GLU cc_start: 0.7518 (tp30) cc_final: 0.7149 (tm-30) REVERT: B 779 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7798 (mtpp) REVERT: B 799 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9023 (tt) REVERT: B 842 GLN cc_start: 0.9303 (tt0) cc_final: 0.8364 (tm-30) REVERT: B 868 ASP cc_start: 0.8092 (m-30) cc_final: 0.7891 (p0) REVERT: B 893 LEU cc_start: 0.8908 (mt) cc_final: 0.8655 (mt) REVERT: B 938 LEU cc_start: 0.8586 (tt) cc_final: 0.7907 (mt) REVERT: B 942 ASN cc_start: 0.8566 (m-40) cc_final: 0.8116 (t0) REVERT: B 988 GLN cc_start: 0.8505 (mt0) cc_final: 0.7974 (mt0) REVERT: B 1015 THR cc_start: 0.7730 (p) cc_final: 0.7386 (p) REVERT: B 1094 LEU cc_start: 0.9477 (mt) cc_final: 0.9179 (tp) REVERT: C 50 VAL cc_start: 0.6633 (m) cc_final: 0.6274 (m) REVERT: C 58 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5963 (t80) REVERT: C 296 ILE cc_start: 0.7207 (mt) cc_final: 0.6984 (mm) REVERT: C 352 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: C 696 MET cc_start: 0.6603 (mmm) cc_final: 0.5559 (tpt) REVERT: C 697 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5443 (tp) REVERT: C 722 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6989 (pt) REVERT: C 794 TYR cc_start: 0.7733 (t80) cc_final: 0.7443 (t80) REVERT: C 815 GLN cc_start: 0.8532 (mt0) cc_final: 0.8160 (tm-30) REVERT: C 827 PHE cc_start: 0.8274 (m-80) cc_final: 0.7925 (m-10) REVERT: C 831 ILE cc_start: 0.8932 (mm) cc_final: 0.8509 (mm) REVERT: C 913 MET cc_start: 0.8009 (tpt) cc_final: 0.7628 (tmm) REVERT: C 1082 VAL cc_start: 0.9603 (t) cc_final: 0.9370 (p) REVERT: C 1089 SER cc_start: 0.9141 (t) cc_final: 0.8585 (p) outliers start: 170 outliers final: 41 residues processed: 830 average time/residue: 0.1832 time to fit residues: 240.8246 Evaluate side-chains 400 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS A 599 GLN A 719 ASN A 800 GLN A 812 ASN A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN A1084 GLN B 298 HIS B 348 HIS ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B 599 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN B 812 ASN B 839 ASN B 842 GLN B1023 GLN B1066 GLN ** B1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 167 HIS C 348 HIS C 436 ASN C 599 GLN C 792 GLN C 812 ASN C1023 GLN C1084 GLN C1177 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.128297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.104497 restraints weight = 187165.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.103451 restraints weight = 125820.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104906 restraints weight = 94401.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105450 restraints weight = 66366.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105912 restraints weight = 60885.276| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 27062 Z= 0.259 Angle : 1.111 14.985 36819 Z= 0.574 Chirality : 0.059 0.362 4131 Planarity : 0.008 0.167 4750 Dihedral : 8.705 58.521 3712 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.36 % Favored : 87.08 % Rotamer: Outliers : 0.31 % Allowed : 3.22 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.62 % Twisted Proline : 0.00 % Twisted General : 1.26 % 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: -3.08 (0.13), residues: 3392 helix: -1.48 (0.16), residues: 676 sheet: -0.65 (0.22), residues: 596 loop : -2.83 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 887 TYR 0.046 0.003 TYR B 641 PHE 0.053 0.003 PHE C 341 TRP 0.035 0.002 TRP B 310 HIS 0.012 0.001 HIS B1146 Details of bonding type rmsd covalent geometry : bond 0.00562 (27022) covalent geometry : angle 1.10826 (36747) SS BOND : bond 0.00799 ( 36) SS BOND : angle 2.19118 ( 72) hydrogen bonds : bond 0.05285 ( 834) hydrogen bonds : angle 6.88065 ( 2226) Misc. bond : bond 0.00874 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 464 time to evaluate : 1.001 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.7841 (m) cc_final: 0.7385 (t) REVERT: A 271 VAL cc_start: 0.6982 (t) cc_final: 0.6764 (t) REVERT: A 303 ILE cc_start: 0.7860 (pt) cc_final: 0.7496 (pt) REVERT: A 351 TYR cc_start: 0.6759 (m-10) cc_final: 0.6139 (m-10) REVERT: A 563 MET cc_start: 0.3170 (tpp) cc_final: 0.2964 (tpp) REVERT: A 682 ILE cc_start: 0.7279 (pt) cc_final: 0.6952 (tp) REVERT: A 757 MET cc_start: 0.8215 (tpt) cc_final: 0.7812 (mmt) REVERT: A 819 GLN cc_start: 0.8741 (mp10) cc_final: 0.8474 (mp10) REVERT: A 820 LEU cc_start: 0.8734 (mt) cc_final: 0.8297 (mt) REVERT: A 896 ASP cc_start: 0.7656 (p0) cc_final: 0.7363 (t0) REVERT: A 906 MET cc_start: 0.7051 (ttt) cc_final: 0.6826 (ttt) REVERT: B 284 LEU cc_start: 0.7605 (mp) cc_final: 0.7260 (mp) REVERT: B 466 GLN cc_start: 0.7107 (mt0) cc_final: 0.6569 (mt0) REVERT: B 569 MET cc_start: 0.5960 (ttm) cc_final: 0.5059 (mtm) REVERT: B 668 LYS cc_start: 0.8154 (tptp) cc_final: 0.7818 (mmmt) REVERT: B 799 ILE cc_start: 0.8830 (mp) cc_final: 0.8039 (mt) REVERT: B 988 GLN cc_start: 0.8074 (mt0) cc_final: 0.7729 (mt0) REVERT: B 1090 GLU cc_start: 0.7817 (tp30) cc_final: 0.7380 (tp30) REVERT: B 1094 LEU cc_start: 0.9076 (mt) cc_final: 0.8860 (tp) REVERT: B 1137 MET cc_start: 0.7264 (mmm) cc_final: 0.6927 (mmm) REVERT: C 256 ILE cc_start: 0.8221 (tt) cc_final: 0.7970 (mt) REVERT: C 563 MET cc_start: 0.3140 (tpt) cc_final: 0.2457 (tpt) REVERT: C 661 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8085 (m) REVERT: C 778 PHE cc_start: 0.7441 (m-80) cc_final: 0.7203 (m-80) REVERT: C 794 TYR cc_start: 0.7356 (t80) cc_final: 0.7094 (t80) REVERT: C 807 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7526 (pttm) REVERT: C 1179 ARG cc_start: 0.5199 (mtt180) cc_final: 0.4931 (mtm-85) REVERT: C 1186 TYR cc_start: 0.4443 (m-80) cc_final: 0.4084 (m-10) outliers start: 9 outliers final: 3 residues processed: 471 average time/residue: 0.1789 time to fit residues: 135.7046 Evaluate side-chains 303 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 299 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 136 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 240 optimal weight: 40.0000 chunk 149 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 421 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1023 GLN A1176 ASN ** A1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 ASN B1023 GLN B1104 ASN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 833 GLN C1084 GLN C1176 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.124900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100990 restraints weight = 217776.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.101213 restraints weight = 165614.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102983 restraints weight = 117280.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103428 restraints weight = 77902.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.104182 restraints weight = 71021.738| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 27062 Z= 0.247 Angle : 1.052 15.335 36819 Z= 0.538 Chirality : 0.057 0.298 4131 Planarity : 0.007 0.112 4750 Dihedral : 8.053 55.860 3712 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.45 % Favored : 86.20 % Rotamer: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.62 % Twisted Proline : 1.36 % Twisted General : 0.86 % 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: -2.83 (0.13), residues: 3392 helix: -0.94 (0.18), residues: 685 sheet: -0.64 (0.22), residues: 574 loop : -2.73 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1179 TYR 0.042 0.003 TYR A 648 PHE 0.050 0.003 PHE C 341 TRP 0.027 0.002 TRP B 310 HIS 0.009 0.002 HIS B1146 Details of bonding type rmsd covalent geometry : bond 0.00539 (27022) covalent geometry : angle 1.04693 (36747) SS BOND : bond 0.00651 ( 36) SS BOND : angle 2.61513 ( 72) hydrogen bonds : bond 0.04934 ( 834) hydrogen bonds : angle 6.57311 ( 2226) Misc. bond : bond 0.00428 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 1.028 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.7774 (m) cc_final: 0.7254 (t) REVERT: A 271 VAL cc_start: 0.7096 (t) cc_final: 0.6864 (t) REVERT: A 563 MET cc_start: 0.2632 (tpp) cc_final: 0.2422 (tpp) REVERT: A 682 ILE cc_start: 0.7374 (pt) cc_final: 0.7174 (tp) REVERT: A 757 MET cc_start: 0.8094 (tpt) cc_final: 0.7701 (tpp) REVERT: A 940 ASP cc_start: 0.4865 (m-30) cc_final: 0.4514 (m-30) REVERT: B 84 MET cc_start: 0.7952 (ttp) cc_final: 0.7679 (mtm) REVERT: B 466 GLN cc_start: 0.7414 (mt0) cc_final: 0.7173 (mt0) REVERT: B 563 MET cc_start: 0.5605 (mmp) cc_final: 0.4014 (mtm) REVERT: B 569 MET cc_start: 0.6108 (ttm) cc_final: 0.5665 (tpp) REVERT: B 757 MET cc_start: 0.7861 (tpp) cc_final: 0.7520 (tpt) REVERT: B 826 GLN cc_start: 0.8152 (pm20) cc_final: 0.7951 (pm20) REVERT: B 996 LEU cc_start: 0.7006 (mt) cc_final: 0.6627 (mp) REVERT: C 238 THR cc_start: 0.7188 (p) cc_final: 0.6868 (p) REVERT: C 347 LEU cc_start: 0.9167 (mm) cc_final: 0.8870 (mt) REVERT: C 563 MET cc_start: 0.2703 (tpt) cc_final: 0.2000 (tpt) REVERT: C 827 PHE cc_start: 0.8235 (m-80) cc_final: 0.7802 (m-10) REVERT: C 1105 GLU cc_start: 0.7557 (tp30) cc_final: 0.7195 (tm-30) REVERT: C 1186 TYR cc_start: 0.4752 (m-80) cc_final: 0.4149 (m-10) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.1665 time to fit residues: 110.7583 Evaluate side-chains 259 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 323 optimal weight: 7.9990 chunk 54 optimal weight: 40.0000 chunk 268 optimal weight: 40.0000 chunk 299 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 273 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 327 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 188 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 GLN A1146 HIS ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 ASN B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.100439 restraints weight = 204051.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099761 restraints weight = 145522.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100817 restraints weight = 122365.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.101248 restraints weight = 83252.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101856 restraints weight = 73334.404| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27062 Z= 0.208 Angle : 0.975 13.673 36819 Z= 0.499 Chirality : 0.054 0.297 4131 Planarity : 0.006 0.104 4750 Dihedral : 7.689 49.973 3712 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.92 % Favored : 86.79 % Rotamer: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.00 % 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: 3392 helix: -0.62 (0.18), residues: 684 sheet: -0.89 (0.21), residues: 618 loop : -2.67 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 841 TYR 0.042 0.002 TYR A 641 PHE 0.058 0.002 PHE C 764 TRP 0.022 0.002 TRP B 310 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00455 (27022) covalent geometry : angle 0.97165 (36747) SS BOND : bond 0.00313 ( 36) SS BOND : angle 2.13624 ( 72) hydrogen bonds : bond 0.04513 ( 834) hydrogen bonds : angle 6.29915 ( 2226) Misc. bond : bond 0.00584 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.8092 (m) cc_final: 0.7613 (t) REVERT: A 271 VAL cc_start: 0.7336 (t) cc_final: 0.7056 (t) REVERT: A 563 MET cc_start: 0.3408 (tpp) cc_final: 0.3155 (tpp) REVERT: A 757 MET cc_start: 0.8139 (tpt) cc_final: 0.7716 (tpp) REVERT: A 819 GLN cc_start: 0.8824 (mp10) cc_final: 0.8617 (mp-120) REVERT: A 940 ASP cc_start: 0.4940 (m-30) cc_final: 0.4692 (m-30) REVERT: B 84 MET cc_start: 0.8022 (ttp) cc_final: 0.7661 (mtm) REVERT: B 284 LEU cc_start: 0.7779 (mp) cc_final: 0.7532 (mp) REVERT: B 569 MET cc_start: 0.6206 (ttm) cc_final: 0.5820 (pmm) REVERT: B 696 MET cc_start: 0.6651 (mmm) cc_final: 0.6296 (mmm) REVERT: B 940 ASP cc_start: 0.6157 (m-30) cc_final: 0.5890 (m-30) REVERT: C 238 THR cc_start: 0.7501 (p) cc_final: 0.7201 (p) REVERT: C 361 TYR cc_start: 0.8890 (m-10) cc_final: 0.8648 (m-10) REVERT: C 563 MET cc_start: 0.2131 (tpt) cc_final: 0.1482 (tpt) REVERT: C 807 LYS cc_start: 0.8113 (tttm) cc_final: 0.7170 (pttm) REVERT: C 820 LEU cc_start: 0.8605 (mt) cc_final: 0.8270 (mp) REVERT: C 827 PHE cc_start: 0.8350 (m-80) cc_final: 0.7954 (m-80) REVERT: C 831 ILE cc_start: 0.8928 (mm) cc_final: 0.8704 (mm) REVERT: C 939 MET cc_start: 0.7709 (mtt) cc_final: 0.7498 (mtp) REVERT: C 1008 MET cc_start: 0.7652 (tmm) cc_final: 0.6901 (tmm) REVERT: C 1034 SER cc_start: 0.8016 (p) cc_final: 0.7738 (t) REVERT: C 1105 GLU cc_start: 0.7525 (tp30) cc_final: 0.6679 (tp30) REVERT: C 1179 ARG cc_start: 0.6014 (mtt180) cc_final: 0.5518 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.1619 time to fit residues: 99.3506 Evaluate side-chains 259 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 155 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 108 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN B1201 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.106532 restraints weight = 228503.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.106476 restraints weight = 220733.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.108494 restraints weight = 152643.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108428 restraints weight = 103263.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109324 restraints weight = 95134.159| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27062 Z= 0.189 Angle : 0.948 12.972 36819 Z= 0.482 Chirality : 0.053 0.268 4131 Planarity : 0.006 0.104 4750 Dihedral : 7.384 47.976 3712 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.75 % Favored : 85.96 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.62 % Twisted Proline : 0.68 % Twisted General : 0.71 % 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 (0.13), residues: 3392 helix: -0.46 (0.19), residues: 683 sheet: -0.99 (0.21), residues: 641 loop : -2.62 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 887 TYR 0.047 0.002 TYR B 648 PHE 0.045 0.002 PHE C 341 TRP 0.020 0.002 TRP B 310 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00407 (27022) covalent geometry : angle 0.94507 (36747) SS BOND : bond 0.00335 ( 36) SS BOND : angle 1.96099 ( 72) hydrogen bonds : bond 0.04340 ( 834) hydrogen bonds : angle 6.14904 ( 2226) Misc. bond : bond 0.00708 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.878 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 TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.7882 (m) cc_final: 0.7378 (t) REVERT: A 271 VAL cc_start: 0.7389 (t) cc_final: 0.7116 (t) REVERT: A 563 MET cc_start: 0.2814 (tpp) cc_final: 0.2549 (tpp) REVERT: A 648 TYR cc_start: 0.6391 (t80) cc_final: 0.5946 (t80) REVERT: A 757 MET cc_start: 0.8008 (tpt) cc_final: 0.7584 (tpp) REVERT: B 161 MET cc_start: 0.7049 (mpp) cc_final: 0.6669 (mmm) REVERT: B 284 LEU cc_start: 0.7715 (mp) cc_final: 0.7476 (mp) REVERT: B 569 MET cc_start: 0.6115 (ttm) cc_final: 0.5865 (pmm) REVERT: B 616 VAL cc_start: 0.8077 (m) cc_final: 0.7819 (p) REVERT: B 1105 GLU cc_start: 0.8042 (tp30) cc_final: 0.7840 (tp30) REVERT: C 238 THR cc_start: 0.7391 (p) cc_final: 0.7182 (p) REVERT: C 696 MET cc_start: 0.7093 (mtp) cc_final: 0.6464 (mtp) REVERT: C 827 PHE cc_start: 0.8350 (m-80) cc_final: 0.7828 (m-80) REVERT: C 831 ILE cc_start: 0.8949 (mm) cc_final: 0.8692 (mm) REVERT: C 1034 SER cc_start: 0.7686 (p) cc_final: 0.7437 (t) REVERT: C 1087 VAL cc_start: 0.9330 (t) cc_final: 0.9066 (t) REVERT: C 1105 GLU cc_start: 0.7534 (tp30) cc_final: 0.7126 (tp30) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1504 time to fit residues: 89.2569 Evaluate side-chains 245 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 233 optimal weight: 9.9990 chunk 271 optimal weight: 50.0000 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 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 516 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 HIS B 769 GLN B 842 GLN B 993 ASN B1104 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 ASN C1079 ASN C1084 GLN C1201 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.121148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096952 restraints weight = 179424.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.096069 restraints weight = 131530.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097559 restraints weight = 104401.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097427 restraints weight = 76368.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.098162 restraints weight = 68203.471| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 27062 Z= 0.258 Angle : 1.008 15.691 36819 Z= 0.515 Chirality : 0.056 0.345 4131 Planarity : 0.006 0.098 4750 Dihedral : 7.614 45.434 3712 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.16 % Favored : 85.52 % Rotamer: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % 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: -2.82 (0.13), residues: 3392 helix: -0.71 (0.18), residues: 691 sheet: -1.17 (0.21), residues: 625 loop : -2.65 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 841 TYR 0.048 0.002 TYR C 648 PHE 0.078 0.003 PHE A 764 TRP 0.023 0.002 TRP C 310 HIS 0.010 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00565 (27022) covalent geometry : angle 1.00350 (36747) SS BOND : bond 0.00567 ( 36) SS BOND : angle 2.27929 ( 72) hydrogen bonds : bond 0.04570 ( 834) hydrogen bonds : angle 6.31362 ( 2226) Misc. bond : bond 0.00351 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 0.790 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.8231 (m) cc_final: 0.7775 (t) REVERT: A 322 THR cc_start: 0.8260 (p) cc_final: 0.7986 (p) REVERT: A 563 MET cc_start: 0.3342 (tpp) cc_final: 0.2972 (tpp) REVERT: A 648 TYR cc_start: 0.6988 (t80) cc_final: 0.6492 (t80) REVERT: A 691 ARG cc_start: 0.7222 (tpp-160) cc_final: 0.6786 (tpp80) REVERT: A 757 MET cc_start: 0.8171 (tpt) cc_final: 0.7766 (tpp) REVERT: A 817 CYS cc_start: 0.4368 (m) cc_final: 0.4110 (m) REVERT: A 943 MET cc_start: 0.6879 (ttm) cc_final: 0.6674 (tpp) REVERT: B 84 MET cc_start: 0.8269 (ttm) cc_final: 0.8039 (mtm) REVERT: B 161 MET cc_start: 0.7411 (mpp) cc_final: 0.6914 (mmm) REVERT: B 284 LEU cc_start: 0.7734 (mp) cc_final: 0.7510 (mp) REVERT: B 569 MET cc_start: 0.6425 (ttm) cc_final: 0.5881 (pmm) REVERT: B 616 VAL cc_start: 0.8284 (m) cc_final: 0.8012 (p) REVERT: B 663 TYR cc_start: 0.7503 (t80) cc_final: 0.7279 (t80) REVERT: B 938 LEU cc_start: 0.9068 (tt) cc_final: 0.8314 (tt) REVERT: B 1105 GLU cc_start: 0.8011 (tp30) cc_final: 0.7762 (tp30) REVERT: C 238 THR cc_start: 0.7582 (p) cc_final: 0.7353 (p) REVERT: C 563 MET cc_start: 0.2586 (tpt) cc_final: 0.1675 (tpt) REVERT: C 696 MET cc_start: 0.7251 (mtp) cc_final: 0.6664 (mtp) REVERT: C 829 SER cc_start: 0.8878 (t) cc_final: 0.8087 (t) REVERT: C 831 ILE cc_start: 0.9007 (mm) cc_final: 0.8770 (mm) REVERT: C 1034 SER cc_start: 0.8021 (p) cc_final: 0.7796 (t) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.1587 time to fit residues: 86.2538 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS B 769 GLN B 993 ASN B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1177 ASN C1201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104070 restraints weight = 190241.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.102916 restraints weight = 165589.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.104124 restraints weight = 123768.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104455 restraints weight = 91531.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.104942 restraints weight = 85586.572| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27062 Z= 0.199 Angle : 0.960 13.553 36819 Z= 0.488 Chirality : 0.054 0.318 4131 Planarity : 0.006 0.103 4750 Dihedral : 7.334 40.487 3712 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.80 % Favored : 85.96 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.68 % 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: -2.75 (0.14), residues: 3392 helix: -0.46 (0.19), residues: 680 sheet: -1.34 (0.21), residues: 661 loop : -2.61 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 841 TYR 0.039 0.002 TYR C 648 PHE 0.042 0.002 PHE C 341 TRP 0.017 0.002 TRP B 310 HIS 0.014 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00430 (27022) covalent geometry : angle 0.95627 (36747) SS BOND : bond 0.00361 ( 36) SS BOND : angle 2.04840 ( 72) hydrogen bonds : bond 0.04284 ( 834) hydrogen bonds : angle 6.20937 ( 2226) Misc. bond : bond 0.00385 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 1.002 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.8292 (m) cc_final: 0.7833 (t) REVERT: A 261 GLN cc_start: 0.7446 (mp10) cc_final: 0.7012 (mp10) REVERT: A 563 MET cc_start: 0.3621 (tpp) cc_final: 0.3181 (tpp) REVERT: A 627 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7723 (tp40) REVERT: A 648 TYR cc_start: 0.6592 (t80) cc_final: 0.6385 (t80) REVERT: A 691 ARG cc_start: 0.7224 (tpp-160) cc_final: 0.6790 (tpp80) REVERT: A 757 MET cc_start: 0.8061 (tpt) cc_final: 0.7756 (tpp) REVERT: A 874 LEU cc_start: 0.7377 (tp) cc_final: 0.6975 (tt) REVERT: A 1084 GLN cc_start: 0.8489 (pp30) cc_final: 0.8269 (pp30) REVERT: A 1100 LYS cc_start: 0.8054 (tttt) cc_final: 0.7841 (tttt) REVERT: B 161 MET cc_start: 0.7104 (mpp) cc_final: 0.6637 (mmm) REVERT: B 284 LEU cc_start: 0.7701 (mp) cc_final: 0.7480 (mp) REVERT: B 569 MET cc_start: 0.6521 (ttm) cc_final: 0.5922 (pmm) REVERT: B 616 VAL cc_start: 0.8125 (m) cc_final: 0.7821 (p) REVERT: B 731 LEU cc_start: 0.7467 (tt) cc_final: 0.7236 (tp) REVERT: B 733 GLN cc_start: 0.8148 (pp30) cc_final: 0.7717 (pp30) REVERT: B 778 PHE cc_start: 0.5559 (m-80) cc_final: 0.5343 (m-80) REVERT: B 831 ILE cc_start: 0.9412 (mm) cc_final: 0.9209 (mm) REVERT: B 857 GLN cc_start: 0.6080 (mp10) cc_final: 0.5391 (pp30) REVERT: B 1067 ILE cc_start: 0.8926 (mt) cc_final: 0.8701 (tp) REVERT: B 1105 GLU cc_start: 0.7991 (tp30) cc_final: 0.7789 (tp30) REVERT: C 69 ILE cc_start: 0.9272 (tt) cc_final: 0.9013 (mp) REVERT: C 238 THR cc_start: 0.7624 (p) cc_final: 0.7397 (p) REVERT: C 563 MET cc_start: 0.4181 (tpt) cc_final: 0.3169 (tpt) REVERT: C 696 MET cc_start: 0.7142 (mtp) cc_final: 0.6207 (tpp) REVERT: C 820 LEU cc_start: 0.8635 (mt) cc_final: 0.8417 (mt) REVERT: C 829 SER cc_start: 0.8901 (t) cc_final: 0.8235 (t) REVERT: C 1084 GLN cc_start: 0.8738 (pp30) cc_final: 0.8470 (tm-30) REVERT: C 1087 VAL cc_start: 0.9381 (t) cc_final: 0.9167 (t) REVERT: C 1105 GLU cc_start: 0.7401 (tp30) cc_final: 0.6996 (tp30) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1621 time to fit residues: 92.0155 Evaluate side-chains 253 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 261 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 230 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 210 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN B 993 ASN B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.122013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100578 restraints weight = 176479.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.099892 restraints weight = 167747.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.100887 restraints weight = 136752.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.100934 restraints weight = 105833.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.101689 restraints weight = 91448.253| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 27062 Z= 0.267 Angle : 1.017 17.907 36819 Z= 0.519 Chirality : 0.056 0.360 4131 Planarity : 0.006 0.106 4750 Dihedral : 7.578 39.179 3712 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.87 % Favored : 84.81 % Rotamer: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % 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: -2.95 (0.13), residues: 3392 helix: -0.76 (0.18), residues: 697 sheet: -1.38 (0.21), residues: 625 loop : -2.72 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 841 TYR 0.050 0.003 TYR A 648 PHE 0.057 0.003 PHE A 341 TRP 0.028 0.002 TRP C 310 HIS 0.013 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00587 (27022) covalent geometry : angle 1.01321 (36747) SS BOND : bond 0.00409 ( 36) SS BOND : angle 2.27009 ( 72) hydrogen bonds : bond 0.04584 ( 834) hydrogen bonds : angle 6.40407 ( 2226) Misc. bond : bond 0.00448 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.892 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.8223 (m) cc_final: 0.7707 (t) REVERT: A 563 MET cc_start: 0.2843 (tpp) cc_final: 0.2296 (tpp) REVERT: A 627 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7722 (tp40) REVERT: A 691 ARG cc_start: 0.7150 (tpp-160) cc_final: 0.6736 (tpp80) REVERT: A 757 MET cc_start: 0.8068 (tpt) cc_final: 0.7774 (tpp) REVERT: A 818 GLU cc_start: 0.8472 (pm20) cc_final: 0.8172 (pm20) REVERT: A 906 MET cc_start: 0.7193 (mtp) cc_final: 0.6728 (mmm) REVERT: A 1084 GLN cc_start: 0.8401 (pp30) cc_final: 0.8086 (pp30) REVERT: B 161 MET cc_start: 0.6995 (mpp) cc_final: 0.6584 (mmm) REVERT: B 569 MET cc_start: 0.6426 (ttm) cc_final: 0.5777 (mmp) REVERT: B 663 TYR cc_start: 0.7803 (t80) cc_final: 0.7511 (t80) REVERT: B 733 GLN cc_start: 0.8351 (pp30) cc_final: 0.7867 (pp30) REVERT: B 1067 ILE cc_start: 0.8947 (mt) cc_final: 0.8706 (tp) REVERT: B 1184 TRP cc_start: 0.6497 (p-90) cc_final: 0.6225 (p-90) REVERT: C 69 ILE cc_start: 0.9289 (tt) cc_final: 0.9075 (mp) REVERT: C 343 ASP cc_start: 0.7854 (m-30) cc_final: 0.7570 (m-30) REVERT: C 694 ARG cc_start: 0.7278 (tmm160) cc_final: 0.6355 (tpp-160) REVERT: C 829 SER cc_start: 0.8711 (t) cc_final: 0.8225 (t) REVERT: C 831 ILE cc_start: 0.8974 (mm) cc_final: 0.8748 (mm) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.1654 time to fit residues: 85.8758 Evaluate side-chains 231 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 75 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 184 optimal weight: 0.0370 chunk 109 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 31 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.125667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105526 restraints weight = 165278.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.104967 restraints weight = 167060.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.106047 restraints weight = 127494.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.106327 restraints weight = 92678.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106718 restraints weight = 81422.935| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.7684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27062 Z= 0.174 Angle : 0.947 14.668 36819 Z= 0.481 Chirality : 0.053 0.321 4131 Planarity : 0.006 0.108 4750 Dihedral : 7.130 39.273 3712 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.51 % Favored : 86.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % 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: 3392 helix: -0.61 (0.19), residues: 691 sheet: -1.42 (0.20), residues: 703 loop : -2.60 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 841 TYR 0.035 0.002 TYR B 641 PHE 0.041 0.002 PHE B 778 TRP 0.020 0.001 TRP A 253 HIS 0.011 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00374 (27022) covalent geometry : angle 0.94221 (36747) SS BOND : bond 0.00411 ( 36) SS BOND : angle 2.43098 ( 72) hydrogen bonds : bond 0.04134 ( 834) hydrogen bonds : angle 6.16297 ( 2226) Misc. bond : bond 0.00400 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 215 SER cc_start: 0.7963 (m) cc_final: 0.7420 (t) REVERT: A 261 GLN cc_start: 0.7322 (mp10) cc_final: 0.6898 (mm110) REVERT: A 563 MET cc_start: 0.2506 (tpp) cc_final: 0.2045 (tpp) REVERT: A 691 ARG cc_start: 0.7224 (tpp-160) cc_final: 0.6895 (tpp80) REVERT: A 757 MET cc_start: 0.8024 (tpt) cc_final: 0.7442 (mtp) REVERT: A 818 GLU cc_start: 0.8287 (mp0) cc_final: 0.7915 (mm-30) REVERT: A 933 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8801 (tptp) REVERT: A 1084 GLN cc_start: 0.8495 (pp30) cc_final: 0.8064 (pp30) REVERT: A 1100 LYS cc_start: 0.8320 (tttt) cc_final: 0.8014 (tttt) REVERT: B 161 MET cc_start: 0.6764 (mpp) cc_final: 0.6421 (mmm) REVERT: B 569 MET cc_start: 0.6282 (ttm) cc_final: 0.6014 (pmm) REVERT: B 663 TYR cc_start: 0.7586 (t80) cc_final: 0.7301 (t80) REVERT: B 733 GLN cc_start: 0.8155 (pp30) cc_final: 0.7725 (pp30) REVERT: B 857 GLN cc_start: 0.6855 (mp10) cc_final: 0.5540 (pp30) REVERT: B 913 MET cc_start: 0.5977 (tpt) cc_final: 0.5717 (ttt) REVERT: B 1067 ILE cc_start: 0.9054 (mt) cc_final: 0.8801 (tp) REVERT: C 69 ILE cc_start: 0.9257 (tt) cc_final: 0.8963 (mp) REVERT: C 161 MET cc_start: 0.7984 (mpp) cc_final: 0.7752 (mmm) REVERT: C 343 ASP cc_start: 0.8072 (m-30) cc_final: 0.7676 (m-30) REVERT: C 361 TYR cc_start: 0.8900 (m-10) cc_final: 0.8624 (m-10) REVERT: C 563 MET cc_start: 0.3419 (tpt) cc_final: 0.2436 (tpt) REVERT: C 722 LEU cc_start: 0.8325 (pp) cc_final: 0.7880 (tp) REVERT: C 757 MET cc_start: 0.8539 (ttm) cc_final: 0.8278 (ttm) REVERT: C 831 ILE cc_start: 0.9002 (mm) cc_final: 0.8786 (mm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1584 time to fit residues: 86.3738 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 : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 269 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 260 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 313 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 627 GLN B 261 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.126990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.106597 restraints weight = 247009.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.107152 restraints weight = 256124.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109446 restraints weight = 153644.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.109222 restraints weight = 105902.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.110362 restraints weight = 93506.980| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27062 Z= 0.166 Angle : 0.933 15.010 36819 Z= 0.472 Chirality : 0.053 0.290 4131 Planarity : 0.006 0.112 4750 Dihedral : 6.936 38.327 3712 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.40 % 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: 3392 helix: -0.42 (0.19), residues: 698 sheet: -1.23 (0.20), residues: 689 loop : -2.56 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 841 TYR 0.037 0.002 TYR C 641 PHE 0.034 0.002 PHE A 341 TRP 0.019 0.001 TRP A 253 HIS 0.010 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00349 (27022) covalent geometry : angle 0.92869 (36747) SS BOND : bond 0.00311 ( 36) SS BOND : angle 2.24141 ( 72) hydrogen bonds : bond 0.04089 ( 834) hydrogen bonds : angle 6.09243 ( 2226) Misc. bond : bond 0.00395 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6784 Ramachandran restraints generated. 3392 Oldfield, 0 Emsley, 3392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.031 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 TARDY: cannot create tardy model for: "SER C 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.7917 (m) cc_final: 0.7376 (t) REVERT: A 261 GLN cc_start: 0.7067 (mp10) cc_final: 0.6612 (mm110) REVERT: A 563 MET cc_start: 0.2364 (tpp) cc_final: 0.1941 (tpp) REVERT: A 691 ARG cc_start: 0.7029 (tpp-160) cc_final: 0.6828 (tpp80) REVERT: A 1084 GLN cc_start: 0.8354 (pp30) cc_final: 0.8086 (pp30) REVERT: B 161 MET cc_start: 0.6604 (mpp) cc_final: 0.6333 (mmm) REVERT: B 563 MET cc_start: 0.5002 (mmm) cc_final: 0.4593 (tpp) REVERT: B 569 MET cc_start: 0.6226 (ttm) cc_final: 0.5986 (pmm) REVERT: B 663 TYR cc_start: 0.7542 (t80) cc_final: 0.7238 (t80) REVERT: B 733 GLN cc_start: 0.8018 (pp30) cc_final: 0.7610 (pp30) REVERT: B 857 GLN cc_start: 0.6544 (mp10) cc_final: 0.5323 (pp30) REVERT: B 913 MET cc_start: 0.5718 (tpt) cc_final: 0.5514 (ttt) REVERT: C 161 MET cc_start: 0.7888 (mpp) cc_final: 0.7672 (mmm) REVERT: C 278 MET cc_start: 0.7094 (ttm) cc_final: 0.6660 (ttm) REVERT: C 343 ASP cc_start: 0.7803 (m-30) cc_final: 0.7424 (m-30) REVERT: C 563 MET cc_start: 0.3223 (tpt) cc_final: 0.2382 (tpt) REVERT: C 606 TYR cc_start: 0.7508 (p90) cc_final: 0.7268 (p90) REVERT: C 694 ARG cc_start: 0.7249 (tmm160) cc_final: 0.6139 (ttt-90) REVERT: C 722 LEU cc_start: 0.8056 (pp) cc_final: 0.7709 (tp) REVERT: C 757 MET cc_start: 0.8441 (ttm) cc_final: 0.7994 (ttt) REVERT: C 831 ILE cc_start: 0.8952 (mm) cc_final: 0.8659 (mm) REVERT: C 1010 THR cc_start: 0.8458 (p) cc_final: 0.8227 (p) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1665 time to fit residues: 90.5913 Evaluate side-chains 249 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 167 optimal weight: 40.0000 chunk 120 optimal weight: 20.0000 chunk 269 optimal weight: 30.0000 chunk 303 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 273 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 310 optimal weight: 0.3980 chunk 304 optimal weight: 2.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN B1104 ASN ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C1009 GLN C1129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.124259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104647 restraints weight = 237924.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.105987 restraints weight = 268741.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107809 restraints weight = 141341.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107868 restraints weight = 97774.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.108660 restraints weight = 84723.260| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.8060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27062 Z= 0.206 Angle : 0.952 14.991 36819 Z= 0.483 Chirality : 0.053 0.328 4131 Planarity : 0.006 0.108 4750 Dihedral : 7.010 37.957 3712 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.10 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.40 % 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: -2.73 (0.14), residues: 3392 helix: -0.50 (0.19), residues: 703 sheet: -1.40 (0.20), residues: 673 loop : -2.57 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 841 TYR 0.038 0.002 TYR B 641 PHE 0.034 0.002 PHE A 341 TRP 0.021 0.002 TRP C 310 HIS 0.012 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00451 (27022) covalent geometry : angle 0.94839 (36747) SS BOND : bond 0.00369 ( 36) SS BOND : angle 2.16678 ( 72) hydrogen bonds : bond 0.04223 ( 834) hydrogen bonds : angle 6.14292 ( 2226) Misc. bond : bond 0.00592 ( 4) =============================================================================== Job complete usr+sys time: 4851.16 seconds wall clock time: 84 minutes 54.26 seconds (5094.26 seconds total)