Starting phenix.real_space_refine on Wed Nov 19 19:07:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x59_6704/11_2025/5x59_6704.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17037 2.51 5 N 4401 2.21 5 O 5247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 6 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: 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} 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': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 11.80, per 1000 atoms: 0.44 Number of scatterers: 26838 At special positions: 0 Unit cell: (152.1, 166.4, 179.4, 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 5247 8.00 N 4401 7.00 C 17037 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=2.04 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.04 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 Atom "HETATM26570 O5 NAG B1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26710 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26430 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26822 O5 NAG C1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26542 O5 NAG A1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26682 O5 NAG B1409 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 2.3 seconds 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 23.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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: 3.676A 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 342 through 350 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: 3.826A 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: 3.924A 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: 3.676A 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: 3.560A 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: 3.638A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.924A 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: 4.471A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.974A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.718A 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 342 through 350 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: 3.612A 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: 3.548A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.973A 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 1062 through 1107 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.073A 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: 6.818A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.858A 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: 6.252A 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: 4.072A 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: 3.547A 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: 7.160A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.823A 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 404 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 407 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 513 through 515 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: 4.598A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.561A 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: 6.251A 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: 4.073A 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: 3.548A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.303A 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: 6.789A 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: 4.322A 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: 4.597A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.464A 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: 3.563A 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 840 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4490 1.32 - 1.45: 7986 1.45 - 1.58: 14761 1.58 - 1.71: 3 1.71 - 1.84: 201 Bond restraints: 27441 Sorted by residual: bond pdb=" N PRO A 59 " pdb=" CD PRO A 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO B 59 " pdb=" CD PRO B 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.69e+01 bond pdb=" CA HIS C 486 " pdb=" C HIS C 486 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.07e+01 bond pdb=" CA HIS B 486 " pdb=" C HIS B 486 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.05e+01 ... (remaining 27436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.12: 36700 5.12 - 10.23: 501 10.23 - 15.35: 86 15.35 - 20.47: 24 20.47 - 25.58: 3 Bond angle restraints: 37314 Sorted by residual: angle pdb=" C SER B1151 " pdb=" N ALA B1152 " pdb=" CA ALA B1152 " ideal model delta sigma weight residual 121.70 140.18 -18.48 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C SER A1151 " pdb=" N ALA A1152 " pdb=" CA ALA A1152 " ideal model delta sigma weight residual 121.70 140.17 -18.47 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 121.70 140.15 -18.45 1.80e+00 3.09e-01 1.05e+02 angle pdb=" N SER A 350 " pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 angle pdb=" N SER C 350 " pdb=" CA SER C 350 " pdb=" C SER C 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 ... (remaining 37309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15944 26.90 - 53.80: 657 53.80 - 80.71: 76 80.71 - 107.61: 9 107.61 - 134.51: 18 Dihedral angle restraints: 16704 sinusoidal: 6714 harmonic: 9990 Sorted by residual: dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.49 -134.51 0 5.00e+00 4.00e-02 7.24e+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 -45.50 -134.50 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.53 -134.47 0 5.00e+00 4.00e-02 7.23e+02 ... (remaining 16701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3415 0.089 - 0.177: 651 0.177 - 0.266: 140 0.266 - 0.355: 33 0.355 - 0.444: 12 Chirality restraints: 4251 Sorted by residual: chirality pdb=" CA ALA C1018 " pdb=" N ALA C1018 " pdb=" C ALA C1018 " pdb=" CB ALA C1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ALA A1018 " pdb=" N ALA A1018 " pdb=" C ALA A1018 " pdb=" CB ALA A1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ALA B1018 " pdb=" N ALA B1018 " pdb=" C ALA B1018 " pdb=" CB ALA B1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4248 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN A 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN A 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN A 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN B 280 " 0.091 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 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.025 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" CD GLN C 280 " 0.090 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 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 75 2.16 - 2.85: 9668 2.85 - 3.53: 36090 3.53 - 4.22: 66762 4.22 - 4.90: 109335 Nonbonded interactions: 221930 Sorted by model distance: nonbonded pdb=" OE1 GLN B 627 " pdb=" CG2 VAL C 271 " model vdw 1.477 3.460 nonbonded pdb=" OE1 GLN A 627 " pdb=" CG2 VAL B 271 " model vdw 1.498 3.460 nonbonded pdb=" OH TYR B 351 " pdb=" CE1 TYR B 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR A 351 " pdb=" CE1 TYR A 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR C 351 " pdb=" CE1 TYR C 361 " model vdw 1.508 3.340 ... (remaining 221925 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.250 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.330 Find NCS groups from input model: 0.250 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4126 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 : 0.012 0.584 27480 Z= 0.815 Angle : 1.714 28.949 37386 Z= 0.964 Chirality : 0.080 0.444 4251 Planarity : 0.009 0.114 4779 Dihedral : 15.224 134.510 10212 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 1.33 % Allowed : 13.22 % Favored : 85.45 % Rotamer: Outliers : 4.97 % Allowed : 7.13 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.22 % Twisted Proline : 0.00 % Twisted General : 1.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.12), residues: 3390 helix: -3.00 (0.13), residues: 675 sheet: -1.20 (0.20), residues: 639 loop : -3.02 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 119 TYR 0.046 0.004 TYR C1171 PHE 0.038 0.004 PHE C1172 TRP 0.032 0.005 TRP B 960 HIS 0.016 0.004 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.01088 (27441) covalent geometry : angle 1.66417 (37314) SS BOND : bond 0.01443 ( 36) SS BOND : angle 9.45726 ( 72) hydrogen bonds : bond 0.15606 ( 840) hydrogen bonds : angle 10.43412 ( 2241) Misc. bond : bond 0.58398 ( 3) *********************** 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 764 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 619 time to evaluate : 0.973 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7898 (mm) cc_final: 0.7690 (mm) REVERT: A 244 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.5156 (m-40) REVERT: A 614 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7639 (mtp-110) REVERT: A 676 SER cc_start: 0.6027 (m) cc_final: 0.5599 (p) REVERT: A 677 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.5949 (t) REVERT: A 682 ILE cc_start: 0.6125 (pp) cc_final: 0.5753 (tp) REVERT: A 719 ASN cc_start: 0.5494 (m-40) cc_final: 0.5252 (m-40) REVERT: A 726 ASP cc_start: 0.5900 (p0) cc_final: 0.5480 (p0) REVERT: A 827 PHE cc_start: 0.6338 (m-80) cc_final: 0.6087 (m-80) REVERT: A 891 GLU cc_start: 0.7436 (tt0) cc_final: 0.7182 (tt0) REVERT: A 895 PHE cc_start: 0.7791 (m-80) cc_final: 0.7570 (m-80) REVERT: A 900 ILE cc_start: 0.4929 (mp) cc_final: 0.4409 (pt) REVERT: A 907 GLN cc_start: 0.6754 (mt0) cc_final: 0.6541 (pm20) REVERT: A 988 GLN cc_start: 0.8280 (mt0) cc_final: 0.8009 (mt0) REVERT: A 993 ASN cc_start: 0.8197 (m-40) cc_final: 0.6919 (p0) REVERT: A 1079 ASN cc_start: 0.7890 (t0) cc_final: 0.7607 (m-40) REVERT: B 357 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6432 (mm-30) REVERT: B 473 PHE cc_start: -0.0684 (OUTLIER) cc_final: -0.1192 (t80) REVERT: B 495 LEU cc_start: 0.1133 (OUTLIER) cc_final: 0.0405 (mm) REVERT: B 565 GLU cc_start: 0.3796 (OUTLIER) cc_final: 0.3534 (mt-10) REVERT: B 662 ILE cc_start: 0.4185 (mm) cc_final: 0.3860 (mm) REVERT: B 718 VAL cc_start: 0.6102 (t) cc_final: 0.5852 (t) REVERT: B 807 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6174 (tmtt) REVERT: B 826 GLN cc_start: 0.7221 (mt0) cc_final: 0.7015 (pm20) REVERT: B 848 ASN cc_start: 0.8103 (t160) cc_final: 0.7766 (t0) REVERT: B 1098 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 1203 LYS cc_start: 0.8231 (mttt) cc_final: 0.7899 (tptt) REVERT: C 487 ASN cc_start: 0.3113 (OUTLIER) cc_final: 0.2768 (p0) REVERT: C 489 THR cc_start: 0.3050 (OUTLIER) cc_final: 0.2768 (m) REVERT: C 587 LYS cc_start: 0.4277 (ptmt) cc_final: 0.3768 (tptt) REVERT: C 667 THR cc_start: 0.4942 (p) cc_final: 0.1360 (m) REVERT: C 970 ILE cc_start: 0.5233 (OUTLIER) cc_final: 0.4557 (mt) REVERT: C 990 LEU cc_start: 0.6186 (mt) cc_final: 0.5842 (mp) REVERT: C 992 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6424 (pt0) REVERT: C 1067 ILE cc_start: 0.7840 (mt) cc_final: 0.7417 (mm) REVERT: C 1089 SER cc_start: 0.8468 (t) cc_final: 0.8058 (t) REVERT: C 1098 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.6916 (tp) REVERT: C 1126 PHE cc_start: 0.3930 (m-80) cc_final: 0.3136 (m-10) outliers start: 145 outliers final: 33 residues processed: 746 average time/residue: 0.1892 time to fit residues: 220.4233 Evaluate side-chains 411 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 368 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 167 HIS ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 599 GLN A 602 ASN A 792 GLN A 812 ASN A 836 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A 870 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 599 GLN B 602 ASN B 792 GLN B 800 GLN B 808 GLN B 832 ASN B 839 ASN B 842 GLN B 848 ASN B 870 ASN B1009 GLN B1028 ASN B1072 ASN B1104 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 602 ASN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 812 ASN C 832 ASN C 842 GLN C 870 ASN C1023 GLN C1028 ASN C1104 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.228917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.204200 restraints weight = 105562.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.206823 restraints weight = 148443.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.210176 restraints weight = 74198.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.209671 restraints weight = 54513.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.210576 restraints weight = 46515.688| |-----------------------------------------------------------------------------| r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4569 r_free = 0.4569 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4569 r_free = 0.4569 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 27480 Z= 0.240 Angle : 1.098 15.966 37386 Z= 0.555 Chirality : 0.059 0.370 4251 Planarity : 0.007 0.114 4779 Dihedral : 10.840 102.277 4427 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.71 % Favored : 88.05 % Rotamer: Outliers : 3.73 % Allowed : 13.70 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.13), residues: 3390 helix: -1.33 (0.17), residues: 684 sheet: -0.83 (0.21), residues: 591 loop : -2.89 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 335 TYR 0.036 0.003 TYR B1153 PHE 0.043 0.003 PHE C 327 TRP 0.036 0.002 TRP B 310 HIS 0.013 0.002 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00526 (27441) covalent geometry : angle 1.09650 (37314) SS BOND : bond 0.00779 ( 36) SS BOND : angle 1.69706 ( 72) hydrogen bonds : bond 0.04932 ( 840) hydrogen bonds : angle 6.55884 ( 2241) Misc. bond : bond 0.00147 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 422 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8383 (mm) cc_final: 0.8132 (mm) REVERT: A 587 LYS cc_start: 0.6400 (ptmt) cc_final: 0.5208 (tppt) REVERT: A 633 ASP cc_start: 0.7191 (t0) cc_final: 0.6438 (p0) REVERT: A 841 ARG cc_start: 0.6850 (mtp-110) cc_final: 0.6259 (ptm-80) REVERT: A 993 ASN cc_start: 0.6902 (m-40) cc_final: 0.6579 (p0) REVERT: A 1100 LYS cc_start: 0.8024 (tttt) cc_final: 0.7807 (tttt) REVERT: A 1129 ASN cc_start: 0.7161 (t0) cc_final: 0.6782 (t0) REVERT: B 65 SER cc_start: 0.8604 (p) cc_final: 0.8124 (m) REVERT: B 85 TYR cc_start: 0.8182 (m-80) cc_final: 0.7705 (m-80) REVERT: B 99 LYS cc_start: 0.6203 (mmtm) cc_final: 0.5907 (mmtm) REVERT: B 310 TRP cc_start: 0.5777 (m-90) cc_final: 0.5481 (m-90) REVERT: B 323 PHE cc_start: 0.7559 (m-10) cc_final: 0.7354 (m-10) REVERT: B 473 PHE cc_start: 0.0017 (OUTLIER) cc_final: -0.0930 (t80) REVERT: B 487 ASN cc_start: 0.0004 (OUTLIER) cc_final: -0.2137 (t0) REVERT: B 565 GLU cc_start: 0.3386 (OUTLIER) cc_final: 0.3090 (mt-10) REVERT: B 820 LEU cc_start: 0.7381 (mt) cc_final: 0.6877 (mm) REVERT: B 854 LYS cc_start: 0.7349 (pptt) cc_final: 0.6963 (pptt) REVERT: B 906 MET cc_start: 0.4628 (tpt) cc_final: 0.4230 (tpt) REVERT: B 938 LEU cc_start: 0.8140 (tt) cc_final: 0.7908 (tp) REVERT: B 1169 ASN cc_start: 0.7170 (p0) cc_final: 0.6635 (p0) REVERT: C 58 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5311 (t80) REVERT: C 161 MET cc_start: -0.0631 (mmt) cc_final: -0.1918 (ptm) REVERT: C 587 LYS cc_start: 0.4273 (ptmt) cc_final: 0.3741 (tptt) REVERT: C 599 GLN cc_start: 0.5044 (OUTLIER) cc_final: 0.4273 (mt0) REVERT: C 943 MET cc_start: 0.6678 (ptm) cc_final: 0.6219 (ptm) REVERT: C 970 ILE cc_start: 0.6188 (OUTLIER) cc_final: 0.5971 (mm) REVERT: C 1098 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8263 (tt) outliers start: 109 outliers final: 56 residues processed: 505 average time/residue: 0.1747 time to fit residues: 142.2302 Evaluate side-chains 371 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 308 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 222 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 259 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 225 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 318 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 348 HIS A 733 GLN A 833 GLN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 91 HIS B 167 HIS B 236 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 346 GLN C 733 GLN C 832 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1027 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.229376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.206239 restraints weight = 89691.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.206355 restraints weight = 126304.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.208530 restraints weight = 83616.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.209406 restraints weight = 50450.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.210036 restraints weight = 44061.719| |-----------------------------------------------------------------------------| r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4559 r_free = 0.4559 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4559 r_free = 0.4559 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27480 Z= 0.180 Angle : 0.987 14.754 37386 Z= 0.498 Chirality : 0.053 0.301 4251 Planarity : 0.006 0.102 4779 Dihedral : 8.526 80.116 4380 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.16 % Favored : 87.58 % Rotamer: Outliers : 3.39 % Allowed : 15.96 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.68 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.13), residues: 3390 helix: -0.59 (0.18), residues: 684 sheet: -0.72 (0.21), residues: 612 loop : -2.71 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 307 TYR 0.029 0.002 TYR A 641 PHE 0.034 0.002 PHE A 895 TRP 0.024 0.001 TRP B 310 HIS 0.010 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00376 (27441) covalent geometry : angle 0.98464 (37314) SS BOND : bond 0.00431 ( 36) SS BOND : angle 1.79050 ( 72) hydrogen bonds : bond 0.04465 ( 840) hydrogen bonds : angle 6.20181 ( 2241) Misc. bond : bond 0.00239 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 354 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 LYS cc_start: 0.6517 (ptmt) cc_final: 0.5358 (tppt) REVERT: A 633 ASP cc_start: 0.7025 (t0) cc_final: 0.6296 (p0) REVERT: A 841 ARG cc_start: 0.7109 (mtp-110) cc_final: 0.6448 (ptm-80) REVERT: A 906 MET cc_start: 0.4832 (ttt) cc_final: 0.4515 (ttt) REVERT: A 1079 ASN cc_start: 0.7715 (m-40) cc_final: 0.7375 (m-40) REVERT: A 1100 LYS cc_start: 0.7814 (tttt) cc_final: 0.7609 (ttpp) REVERT: B 310 TRP cc_start: 0.5670 (m-90) cc_final: 0.5390 (m-90) REVERT: B 473 PHE cc_start: -0.0159 (OUTLIER) cc_final: -0.1057 (t80) REVERT: B 565 GLU cc_start: 0.3039 (OUTLIER) cc_final: 0.2690 (mt-10) REVERT: B 665 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7620 (pttp) REVERT: B 807 LYS cc_start: 0.7195 (mtmt) cc_final: 0.6825 (tmtt) REVERT: B 820 LEU cc_start: 0.7411 (mt) cc_final: 0.7180 (mm) REVERT: B 854 LYS cc_start: 0.7377 (pptt) cc_final: 0.7123 (pptt) REVERT: B 938 LEU cc_start: 0.8036 (tt) cc_final: 0.7737 (tp) REVERT: B 943 MET cc_start: 0.7718 (tpp) cc_final: 0.7413 (tpp) REVERT: C 58 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5628 (t80) REVERT: C 161 MET cc_start: 0.0187 (mmt) cc_final: -0.1683 (ptm) REVERT: C 563 MET cc_start: 0.2284 (mmm) cc_final: 0.0966 (mtp) REVERT: C 587 LYS cc_start: 0.4727 (ptmt) cc_final: 0.3970 (tptt) REVERT: C 733 GLN cc_start: 0.2616 (OUTLIER) cc_final: 0.1440 (pm20) REVERT: C 849 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7806 (mt) REVERT: C 1098 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8090 (tp) outliers start: 99 outliers final: 55 residues processed: 425 average time/residue: 0.1696 time to fit residues: 117.4745 Evaluate side-chains 362 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 TYR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 733 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 341 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 271 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 GLN A 993 ASN A1163 ASN B 125 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN B1201 ASN C 670 HIS ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 ASN C1085 GLN ** C1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.217330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.192200 restraints weight = 98769.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.196425 restraints weight = 151389.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.197916 restraints weight = 49934.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.199067 restraints weight = 35073.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.199132 restraints weight = 26104.838| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 27480 Z= 0.236 Angle : 1.010 15.539 37386 Z= 0.518 Chirality : 0.055 0.333 4251 Planarity : 0.007 0.105 4779 Dihedral : 8.051 77.114 4372 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.28 % Favored : 86.42 % Rotamer: Outliers : 3.84 % Allowed : 16.27 % Favored : 79.89 % 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 are not related in a simple way. whole: -2.63 (0.14), residues: 3390 helix: -0.41 (0.19), residues: 687 sheet: -1.00 (0.21), residues: 669 loop : -2.63 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 119 TYR 0.030 0.002 TYR A 641 PHE 0.053 0.003 PHE C 778 TRP 0.025 0.002 TRP B 310 HIS 0.007 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00527 (27441) covalent geometry : angle 1.00807 (37314) SS BOND : bond 0.00927 ( 36) SS BOND : angle 1.83295 ( 72) hydrogen bonds : bond 0.04581 ( 840) hydrogen bonds : angle 6.27668 ( 2241) Misc. bond : bond 0.00249 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 366 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: A 87 TYR cc_start: 0.4265 (m-10) cc_final: 0.3934 (m-10) REVERT: A 587 LYS cc_start: 0.6816 (ptmt) cc_final: 0.5482 (tppt) REVERT: A 633 ASP cc_start: 0.7066 (t0) cc_final: 0.6243 (p0) REVERT: A 659 VAL cc_start: 0.8764 (p) cc_final: 0.8392 (m) REVERT: B 65 SER cc_start: 0.8525 (p) cc_final: 0.8304 (m) REVERT: B 253 TRP cc_start: 0.8541 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: B 310 TRP cc_start: 0.5790 (m-90) cc_final: 0.5403 (m-90) REVERT: B 473 PHE cc_start: 0.0212 (OUTLIER) cc_final: -0.0625 (t80) REVERT: B 565 GLU cc_start: 0.2633 (OUTLIER) cc_final: 0.2201 (mt-10) REVERT: B 715 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6787 (tp) REVERT: C 161 MET cc_start: -0.0454 (mmt) cc_final: -0.1891 (ptm) REVERT: C 240 MET cc_start: 0.0551 (OUTLIER) cc_final: -0.0341 (mtm) REVERT: C 599 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4358 (mt0) REVERT: C 733 GLN cc_start: 0.2460 (OUTLIER) cc_final: 0.1351 (pm20) REVERT: C 1098 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8724 (tp) REVERT: C 1125 SER cc_start: 0.8749 (p) cc_final: 0.8520 (p) outliers start: 112 outliers final: 60 residues processed: 444 average time/residue: 0.1682 time to fit residues: 122.6533 Evaluate side-chains 360 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 670 HIS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 733 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 109 optimal weight: 0.1980 chunk 174 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 GLN A 785 ASN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN B 719 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.214990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188526 restraints weight = 89722.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192581 restraints weight = 139234.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.194542 restraints weight = 52152.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.195217 restraints weight = 35106.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.195527 restraints weight = 28120.447| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4410 r_free = 0.4410 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4410 r_free = 0.4410 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27480 Z= 0.192 Angle : 0.967 16.450 37386 Z= 0.492 Chirality : 0.053 0.364 4251 Planarity : 0.006 0.105 4779 Dihedral : 7.543 72.573 4363 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.36 % Favored : 87.34 % Rotamer: Outliers : 3.43 % Allowed : 18.05 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.14), residues: 3390 helix: 0.00 (0.19), residues: 666 sheet: -0.44 (0.22), residues: 591 loop : -2.72 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 847 TYR 0.026 0.002 TYR A1204 PHE 0.055 0.002 PHE C 778 TRP 0.019 0.001 TRP B 310 HIS 0.039 0.002 HIS C 670 Details of bonding type rmsd covalent geometry : bond 0.00425 (27441) covalent geometry : angle 0.96481 (37314) SS BOND : bond 0.00481 ( 36) SS BOND : angle 1.72043 ( 72) hydrogen bonds : bond 0.04336 ( 840) hydrogen bonds : angle 6.09432 ( 2241) Misc. bond : bond 0.00124 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 338 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: A 180 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6805 (tt) REVERT: A 308 LYS cc_start: 0.4906 (tppt) cc_final: 0.4530 (mtmt) REVERT: A 563 MET cc_start: 0.1898 (ttt) cc_final: 0.1563 (ttp) REVERT: A 587 LYS cc_start: 0.6979 (ptmt) cc_final: 0.5523 (tppt) REVERT: A 633 ASP cc_start: 0.7277 (t0) cc_final: 0.6317 (p0) REVERT: A 659 VAL cc_start: 0.8662 (p) cc_final: 0.8430 (m) REVERT: A 726 ASP cc_start: 0.5143 (p0) cc_final: 0.4845 (p0) REVERT: A 810 VAL cc_start: 0.5857 (OUTLIER) cc_final: 0.5646 (m) REVERT: B 161 MET cc_start: 0.5271 (mpp) cc_final: 0.4220 (ttt) REVERT: B 310 TRP cc_start: 0.5838 (m-90) cc_final: 0.5582 (m-90) REVERT: B 330 ASP cc_start: 0.7084 (p0) cc_final: 0.6797 (t70) REVERT: B 357 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: B 473 PHE cc_start: 0.0277 (OUTLIER) cc_final: -0.0587 (t80) REVERT: B 565 GLU cc_start: 0.2627 (OUTLIER) cc_final: 0.2240 (mt-10) REVERT: B 665 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8226 (pttp) REVERT: B 938 LEU cc_start: 0.8706 (tt) cc_final: 0.8461 (tt) REVERT: B 943 MET cc_start: 0.7655 (tpt) cc_final: 0.7407 (tpp) REVERT: B 1036 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7324 (mm) REVERT: C 58 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7303 (t80) REVERT: C 75 PHE cc_start: 0.5788 (m-10) cc_final: 0.5577 (m-10) REVERT: C 161 MET cc_start: -0.0493 (mmt) cc_final: -0.1706 (ptm) REVERT: C 240 MET cc_start: 0.0546 (OUTLIER) cc_final: -0.0651 (mtm) REVERT: C 510 ASP cc_start: 0.2725 (OUTLIER) cc_final: 0.2498 (m-30) REVERT: C 563 MET cc_start: 0.1929 (mmm) cc_final: -0.0631 (tmm) REVERT: C 633 ASP cc_start: 0.6352 (m-30) cc_final: 0.5298 (p0) REVERT: C 815 GLN cc_start: 0.6083 (mp10) cc_final: 0.5806 (mp10) REVERT: C 1149 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7889 (p) REVERT: C 1174 LYS cc_start: 0.6351 (mttt) cc_final: 0.5268 (tptm) outliers start: 100 outliers final: 63 residues processed: 411 average time/residue: 0.1682 time to fit residues: 113.9363 Evaluate side-chains 368 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 293 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 670 HIS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 870 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 77 optimal weight: 0.0980 chunk 140 optimal weight: 0.7980 chunk 272 optimal weight: 30.0000 chunk 304 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 238 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 283 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 833 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN C 670 HIS ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.213683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.190553 restraints weight = 119992.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.192783 restraints weight = 158256.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.192978 restraints weight = 58425.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.193410 restraints weight = 49459.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.193988 restraints weight = 35093.217| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4390 r_free = 0.4390 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4390 r_free = 0.4390 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 27480 Z= 0.185 Angle : 0.938 13.661 37386 Z= 0.480 Chirality : 0.052 0.292 4251 Planarity : 0.006 0.106 4779 Dihedral : 7.268 70.959 4359 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.81 % Favored : 86.96 % Rotamer: Outliers : 3.49 % Allowed : 19.15 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % 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 are not related in a simple way. whole: -2.46 (0.14), residues: 3390 helix: 0.14 (0.20), residues: 663 sheet: -0.55 (0.22), residues: 591 loop : -2.73 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 841 TYR 0.032 0.002 TYR A 87 PHE 0.039 0.002 PHE A 895 TRP 0.022 0.002 TRP C1184 HIS 0.020 0.002 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00413 (27441) covalent geometry : angle 0.93547 (37314) SS BOND : bond 0.00375 ( 36) SS BOND : angle 1.93068 ( 72) hydrogen bonds : bond 0.04209 ( 840) hydrogen bonds : angle 5.97352 ( 2241) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 327 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9026 (mm) cc_final: 0.8825 (mm) REVERT: A 58 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5793 (m-80) REVERT: A 70 THR cc_start: 0.7822 (m) cc_final: 0.7454 (p) REVERT: A 143 ILE cc_start: 0.7623 (pt) cc_final: 0.7422 (pt) REVERT: A 308 LYS cc_start: 0.5033 (tppt) cc_final: 0.4579 (mtmt) REVERT: A 587 LYS cc_start: 0.6899 (ptmt) cc_final: 0.5480 (tppt) REVERT: A 633 ASP cc_start: 0.7177 (t0) cc_final: 0.6355 (p0) REVERT: A 659 VAL cc_start: 0.8618 (p) cc_final: 0.8226 (m) REVERT: A 726 ASP cc_start: 0.5398 (p0) cc_final: 0.5033 (p0) REVERT: A 940 ASP cc_start: 0.6169 (m-30) cc_final: 0.5922 (m-30) REVERT: A 1067 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6714 (mm) REVERT: A 1171 TYR cc_start: 0.7847 (m-10) cc_final: 0.7591 (m-80) REVERT: B 32 GLU cc_start: 0.4959 (tp30) cc_final: 0.4357 (tp30) REVERT: B 161 MET cc_start: 0.4983 (mpp) cc_final: 0.4079 (ttt) REVERT: B 258 GLN cc_start: 0.6321 (tp40) cc_final: 0.5932 (pp30) REVERT: B 310 TRP cc_start: 0.5842 (m-90) cc_final: 0.5596 (m-90) REVERT: B 473 PHE cc_start: 0.0405 (OUTLIER) cc_final: -0.0506 (t80) REVERT: B 565 GLU cc_start: 0.3054 (OUTLIER) cc_final: 0.2340 (mt-10) REVERT: B 733 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.5291 (pp30) REVERT: B 943 MET cc_start: 0.7283 (tpt) cc_final: 0.7037 (tpp) REVERT: C 58 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 78 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 161 MET cc_start: -0.0298 (mmt) cc_final: -0.2163 (ptm) REVERT: C 240 MET cc_start: 0.0209 (OUTLIER) cc_final: -0.0860 (mtm) REVERT: C 510 ASP cc_start: 0.2617 (OUTLIER) cc_final: 0.2274 (m-30) REVERT: C 563 MET cc_start: 0.1735 (mmm) cc_final: 0.0524 (mtp) REVERT: C 599 GLN cc_start: 0.5554 (OUTLIER) cc_final: 0.5322 (mt0) REVERT: C 633 ASP cc_start: 0.6794 (m-30) cc_final: 0.5717 (p0) REVERT: C 978 TYR cc_start: 0.7884 (m-10) cc_final: 0.7558 (m-10) REVERT: C 1149 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 1174 LYS cc_start: 0.6165 (mttt) cc_final: 0.5168 (tptp) outliers start: 102 outliers final: 69 residues processed: 401 average time/residue: 0.1661 time to fit residues: 109.8289 Evaluate side-chains 362 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 283 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 222 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 306 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 988 GLN A 993 ASN A1084 GLN A1132 ASN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C1016 ASN ** 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 = 0.4552 r_free = 0.4552 target = 0.206210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.182355 restraints weight = 89051.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184927 restraints weight = 151632.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.186167 restraints weight = 52737.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186720 restraints weight = 38929.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.186909 restraints weight = 28124.193| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.8973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27480 Z= 0.224 Angle : 0.995 13.402 37386 Z= 0.507 Chirality : 0.055 0.336 4251 Planarity : 0.006 0.108 4779 Dihedral : 7.527 69.693 4358 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.96 % Favored : 85.74 % Rotamer: Outliers : 3.60 % Allowed : 20.35 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.13), residues: 3390 helix: -0.10 (0.19), residues: 672 sheet: -0.82 (0.22), residues: 582 loop : -2.75 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 887 TYR 0.030 0.002 TYR A 641 PHE 0.037 0.003 PHE A 895 TRP 0.042 0.003 TRP B 960 HIS 0.017 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00510 (27441) covalent geometry : angle 0.99357 (37314) SS BOND : bond 0.00370 ( 36) SS BOND : angle 1.67604 ( 72) hydrogen bonds : bond 0.04303 ( 840) hydrogen bonds : angle 6.14721 ( 2241) Misc. bond : bond 0.00069 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 335 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9146 (mm) cc_final: 0.8832 (mm) REVERT: A 58 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: A 143 ILE cc_start: 0.8082 (pt) cc_final: 0.7875 (pt) REVERT: A 180 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 240 MET cc_start: 0.3661 (tpt) cc_final: -0.0607 (ttt) REVERT: A 267 SER cc_start: 0.8579 (t) cc_final: 0.8154 (p) REVERT: A 308 LYS cc_start: 0.5308 (tppt) cc_final: 0.4351 (mtmm) REVERT: A 563 MET cc_start: 0.2196 (ttt) cc_final: 0.1977 (ttp) REVERT: A 587 LYS cc_start: 0.6874 (ptmt) cc_final: 0.5595 (tppt) REVERT: A 631 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7783 (t) REVERT: A 633 ASP cc_start: 0.7373 (t0) cc_final: 0.6601 (p0) REVERT: A 659 VAL cc_start: 0.8756 (p) cc_final: 0.8488 (m) REVERT: A 729 LEU cc_start: 0.5330 (OUTLIER) cc_final: 0.4941 (mp) REVERT: A 1174 LYS cc_start: 0.5423 (mttt) cc_final: 0.4707 (tptm) REVERT: B 161 MET cc_start: 0.4722 (mpp) cc_final: 0.4147 (ttt) REVERT: B 252 GLU cc_start: 0.7268 (tt0) cc_final: 0.7011 (tp30) REVERT: B 281 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7112 (p90) REVERT: B 310 TRP cc_start: 0.5914 (m-90) cc_final: 0.5662 (m-90) REVERT: B 473 PHE cc_start: 0.0040 (OUTLIER) cc_final: -0.0769 (m-80) REVERT: B 565 GLU cc_start: 0.3404 (OUTLIER) cc_final: 0.2310 (mt-10) REVERT: B 619 ASN cc_start: 0.5931 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: B 733 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6024 (pp30) REVERT: B 943 MET cc_start: 0.7163 (tpt) cc_final: 0.6927 (tpt) REVERT: B 1008 MET cc_start: 0.7381 (tmm) cc_final: 0.7138 (tmm) REVERT: C 58 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 161 MET cc_start: 0.0362 (mmt) cc_final: -0.1377 (ptm) REVERT: C 167 HIS cc_start: 0.4319 (OUTLIER) cc_final: 0.3902 (m90) REVERT: C 180 LEU cc_start: 0.5557 (tt) cc_final: 0.5111 (tt) REVERT: C 240 MET cc_start: 0.0287 (OUTLIER) cc_final: -0.0859 (mtt) REVERT: C 252 GLU cc_start: 0.4750 (pm20) cc_final: 0.4543 (pm20) REVERT: C 563 MET cc_start: 0.1809 (mmm) cc_final: 0.0605 (mtp) REVERT: C 633 ASP cc_start: 0.7093 (m-30) cc_final: 0.6475 (p0) REVERT: C 757 MET cc_start: 0.6620 (tpt) cc_final: 0.6393 (mmm) REVERT: C 960 TRP cc_start: 0.7018 (OUTLIER) cc_final: 0.6582 (t60) REVERT: C 978 TYR cc_start: 0.7931 (m-10) cc_final: 0.7284 (m-10) REVERT: C 1174 LYS cc_start: 0.6041 (mttt) cc_final: 0.5170 (tptp) outliers start: 105 outliers final: 64 residues processed: 410 average time/residue: 0.1675 time to fit residues: 113.1514 Evaluate side-chains 363 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 317 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 176 optimal weight: 0.0770 chunk 164 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN A1085 GLN A1146 HIS B 36 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN C1009 GLN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.208222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.181288 restraints weight = 112915.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.184235 restraints weight = 157869.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.185771 restraints weight = 57714.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.185667 restraints weight = 43118.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186736 restraints weight = 32756.401| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4314 r_free = 0.4314 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4314 r_free = 0.4314 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.9282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27480 Z= 0.173 Angle : 0.926 13.123 37386 Z= 0.471 Chirality : 0.051 0.274 4251 Planarity : 0.006 0.101 4779 Dihedral : 7.099 68.850 4356 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.66 % Favored : 87.10 % Rotamer: Outliers : 2.95 % Allowed : 21.45 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.14), residues: 3390 helix: 0.20 (0.20), residues: 660 sheet: -0.85 (0.21), residues: 603 loop : -2.66 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 887 TYR 0.032 0.002 TYR A 641 PHE 0.036 0.002 PHE A 895 TRP 0.027 0.002 TRP B 253 HIS 0.012 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00378 (27441) covalent geometry : angle 0.92397 (37314) SS BOND : bond 0.00341 ( 36) SS BOND : angle 1.59628 ( 72) hydrogen bonds : bond 0.04089 ( 840) hydrogen bonds : angle 5.91888 ( 2241) Misc. bond : bond 0.00036 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 324 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9115 (mm) cc_final: 0.8865 (mm) REVERT: A 58 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5020 (m-80) REVERT: A 161 MET cc_start: 0.4344 (tpp) cc_final: 0.4034 (mtt) REVERT: A 180 LEU cc_start: 0.8263 (mt) cc_final: 0.7712 (tt) REVERT: A 267 SER cc_start: 0.8451 (t) cc_final: 0.8005 (p) REVERT: A 308 LYS cc_start: 0.5397 (tppt) cc_final: 0.4499 (mtmt) REVERT: A 563 MET cc_start: 0.2169 (ttt) cc_final: 0.1706 (ttp) REVERT: A 587 LYS cc_start: 0.7040 (ptmt) cc_final: 0.5656 (tppt) REVERT: A 631 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 633 ASP cc_start: 0.7332 (t0) cc_final: 0.6595 (p0) REVERT: A 659 VAL cc_start: 0.8620 (p) cc_final: 0.8285 (m) REVERT: A 729 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4818 (mp) REVERT: A 900 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5914 (pt) REVERT: A 1053 ASP cc_start: 0.1476 (m-30) cc_final: 0.0556 (m-30) REVERT: A 1174 LYS cc_start: 0.5093 (mttt) cc_final: 0.4448 (tptp) REVERT: B 161 MET cc_start: 0.4777 (mpp) cc_final: 0.4217 (ttt) REVERT: B 310 TRP cc_start: 0.5889 (m-90) cc_final: 0.5686 (m-10) REVERT: B 473 PHE cc_start: 0.0029 (OUTLIER) cc_final: -0.0678 (m-80) REVERT: B 565 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.2452 (mp0) REVERT: B 733 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.5945 (pp30) REVERT: B 943 MET cc_start: 0.7092 (tpt) cc_final: 0.6875 (tpt) REVERT: B 1186 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.4184 (m-10) REVERT: C 58 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7613 (t80) REVERT: C 161 MET cc_start: 0.0006 (mmt) cc_final: -0.0764 (mmm) REVERT: C 240 MET cc_start: 0.0170 (OUTLIER) cc_final: -0.0855 (mtm) REVERT: C 815 GLN cc_start: 0.6618 (mp10) cc_final: 0.6265 (mp10) REVERT: C 843 ASP cc_start: 0.6930 (m-30) cc_final: 0.6718 (t0) REVERT: C 960 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.6253 (t60) REVERT: C 978 TYR cc_start: 0.7932 (m-10) cc_final: 0.7356 (m-10) REVERT: C 1174 LYS cc_start: 0.5888 (mttt) cc_final: 0.5188 (tptm) outliers start: 86 outliers final: 59 residues processed: 385 average time/residue: 0.1709 time to fit residues: 108.4436 Evaluate side-chains 355 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1186 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 190 optimal weight: 0.9980 chunk 223 optimal weight: 0.0470 chunk 184 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 219 optimal weight: 0.0470 chunk 36 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 842 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 833 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN B1129 ASN C 870 ASN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.209826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185504 restraints weight = 103621.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.186461 restraints weight = 135389.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184756 restraints weight = 57458.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.185216 restraints weight = 46446.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.185873 restraints weight = 31580.548| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4308 r_free = 0.4308 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4308 r_free = 0.4308 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.9488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27480 Z= 0.165 Angle : 0.913 12.872 37386 Z= 0.465 Chirality : 0.051 0.264 4251 Planarity : 0.006 0.105 4779 Dihedral : 6.855 65.930 4354 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.72 % Favored : 87.05 % Rotamer: Outliers : 2.64 % Allowed : 21.93 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.62 % Twisted Proline : 1.36 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3390 helix: 0.11 (0.19), residues: 693 sheet: -1.06 (0.21), residues: 633 loop : -2.53 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.033 0.002 TYR C 641 PHE 0.033 0.002 PHE B 778 TRP 0.025 0.002 TRP B 253 HIS 0.011 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00355 (27441) covalent geometry : angle 0.91091 (37314) SS BOND : bond 0.00250 ( 36) SS BOND : angle 1.69718 ( 72) hydrogen bonds : bond 0.04064 ( 840) hydrogen bonds : angle 5.87957 ( 2241) Misc. bond : bond 0.00723 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 304 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8763 (mm) cc_final: 0.8448 (mm) REVERT: A 58 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: A 180 LEU cc_start: 0.8331 (mt) cc_final: 0.7854 (tt) REVERT: A 290 ILE cc_start: 0.7898 (mt) cc_final: 0.7505 (mm) REVERT: A 308 LYS cc_start: 0.5303 (tppt) cc_final: 0.4398 (mtmm) REVERT: A 563 MET cc_start: 0.1934 (ttt) cc_final: 0.1496 (ttp) REVERT: A 587 LYS cc_start: 0.7082 (ptmt) cc_final: 0.5637 (tppt) REVERT: A 633 ASP cc_start: 0.7300 (t0) cc_final: 0.6669 (p0) REVERT: A 729 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4891 (mp) REVERT: A 892 ASP cc_start: 0.6551 (OUTLIER) cc_final: 0.6259 (t0) REVERT: A 932 TYR cc_start: 0.6824 (p90) cc_final: 0.6392 (p90) REVERT: A 1053 ASP cc_start: 0.0792 (m-30) cc_final: 0.0029 (m-30) REVERT: A 1174 LYS cc_start: 0.4981 (mttt) cc_final: 0.4422 (tptp) REVERT: B 473 PHE cc_start: -0.0065 (OUTLIER) cc_final: -0.0756 (m-80) REVERT: B 619 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.6004 (m-40) REVERT: B 733 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.5647 (pp30) REVERT: B 821 LEU cc_start: 0.7295 (pp) cc_final: 0.6404 (tp) REVERT: B 906 MET cc_start: 0.4994 (tpt) cc_final: 0.4766 (tpt) REVERT: B 1105 GLU cc_start: 0.7334 (pt0) cc_final: 0.7106 (pt0) REVERT: C 58 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7442 (t80) REVERT: C 161 MET cc_start: -0.0680 (mmt) cc_final: -0.1378 (mmm) REVERT: C 240 MET cc_start: 0.0146 (OUTLIER) cc_final: -0.0761 (mtm) REVERT: C 633 ASP cc_start: 0.7125 (t0) cc_final: 0.6026 (p0) REVERT: C 815 GLN cc_start: 0.6498 (mp10) cc_final: 0.6027 (mp10) REVERT: C 960 TRP cc_start: 0.6670 (OUTLIER) cc_final: 0.6198 (t60) REVERT: C 978 TYR cc_start: 0.7884 (m-10) cc_final: 0.7313 (m-10) REVERT: C 1174 LYS cc_start: 0.5472 (mttt) cc_final: 0.5091 (tptm) outliers start: 77 outliers final: 56 residues processed: 361 average time/residue: 0.1725 time to fit residues: 103.2355 Evaluate side-chains 345 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1186 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 230 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 190 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 163 optimal weight: 0.0670 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 769 GLN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN C 848 ASN C 870 ASN ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN C1201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.211394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.186723 restraints weight = 105785.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188820 restraints weight = 148000.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189848 restraints weight = 58785.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.189970 restraints weight = 42932.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190518 restraints weight = 34684.086| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4366 r_free = 0.4366 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4366 r_free = 0.4366 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.9648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27480 Z= 0.163 Angle : 0.920 13.701 37386 Z= 0.466 Chirality : 0.050 0.305 4251 Planarity : 0.006 0.104 4779 Dihedral : 6.615 55.336 4351 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.22 % Favored : 87.52 % Rotamer: Outliers : 2.33 % Allowed : 22.37 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3390 helix: 0.11 (0.19), residues: 708 sheet: -0.94 (0.20), residues: 645 loop : -2.61 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 694 TYR 0.050 0.002 TYR B1141 PHE 0.033 0.002 PHE A 895 TRP 0.046 0.002 TRP B 310 HIS 0.010 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00344 (27441) covalent geometry : angle 0.91821 (37314) SS BOND : bond 0.00268 ( 36) SS BOND : angle 1.72538 ( 72) hydrogen bonds : bond 0.03967 ( 840) hydrogen bonds : angle 5.78704 ( 2241) Misc. bond : bond 0.00295 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 302 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8818 (mm) cc_final: 0.8555 (mm) REVERT: A 58 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: A 161 MET cc_start: 0.4275 (tpp) cc_final: 0.4035 (mtt) REVERT: A 180 LEU cc_start: 0.8293 (mt) cc_final: 0.7895 (tt) REVERT: A 290 ILE cc_start: 0.7784 (mt) cc_final: 0.7457 (mm) REVERT: A 308 LYS cc_start: 0.5268 (tppt) cc_final: 0.4243 (mtmm) REVERT: A 563 MET cc_start: 0.2054 (ttt) cc_final: 0.1618 (ttp) REVERT: A 587 LYS cc_start: 0.7001 (ptmt) cc_final: 0.5634 (tppt) REVERT: A 633 ASP cc_start: 0.7262 (t0) cc_final: 0.6672 (p0) REVERT: A 729 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4779 (mp) REVERT: A 892 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.6022 (t0) REVERT: A 932 TYR cc_start: 0.6883 (p90) cc_final: 0.6652 (p90) REVERT: A 1053 ASP cc_start: 0.1306 (m-30) cc_final: 0.0520 (m-30) REVERT: A 1105 GLU cc_start: 0.6311 (pt0) cc_final: 0.5942 (pm20) REVERT: B 619 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6136 (m-40) REVERT: B 807 LYS cc_start: 0.7849 (tmtt) cc_final: 0.6805 (mttt) REVERT: B 821 LEU cc_start: 0.7300 (pp) cc_final: 0.6396 (tp) REVERT: B 906 MET cc_start: 0.4759 (tpt) cc_final: 0.4498 (tpt) REVERT: C 58 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 161 MET cc_start: -0.1251 (mmt) cc_final: -0.2154 (mmm) REVERT: C 240 MET cc_start: -0.0041 (OUTLIER) cc_final: -0.0740 (mtm) REVERT: C 510 ASP cc_start: 0.2725 (OUTLIER) cc_final: 0.2375 (m-30) REVERT: C 563 MET cc_start: 0.2840 (mmm) cc_final: -0.0806 (tmm) REVERT: C 633 ASP cc_start: 0.7203 (t0) cc_final: 0.5951 (p0) REVERT: C 721 SER cc_start: 0.4240 (OUTLIER) cc_final: 0.3190 (p) REVERT: C 815 GLN cc_start: 0.6333 (mp10) cc_final: 0.5704 (mp10) REVERT: C 960 TRP cc_start: 0.6543 (OUTLIER) cc_final: 0.6005 (t60) REVERT: C 978 TYR cc_start: 0.7771 (m-10) cc_final: 0.7343 (m-10) REVERT: C 1174 LYS cc_start: 0.5266 (mttt) cc_final: 0.4982 (tptm) outliers start: 68 outliers final: 47 residues processed: 354 average time/residue: 0.1616 time to fit residues: 95.0243 Evaluate side-chains 336 residues out of total 2946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 870 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1186 TYR Chi-restraints excluded: chain C residue 1201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 232 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 333 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 286 optimal weight: 10.0000 chunk 175 optimal weight: 0.0570 chunk 96 optimal weight: 5.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 833 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.210908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188046 restraints weight = 95039.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.190970 restraints weight = 147991.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.192399 restraints weight = 50446.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.192858 restraints weight = 36063.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193076 restraints weight = 25467.976| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4388 r_free = 0.4388 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4388 r_free = 0.4388 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.9663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.256 27480 Z= 0.269 Angle : 1.195 59.199 37386 Z= 0.667 Chirality : 0.052 0.533 4251 Planarity : 0.006 0.146 4779 Dihedral : 6.638 55.384 4348 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.30 % Favored : 87.40 % Rotamer: Outliers : 2.26 % Allowed : 22.17 % Favored : 75.57 % Cbeta Deviations : 0.09 % 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 are not related in a simple way. whole: -2.41 (0.14), residues: 3390 helix: 0.10 (0.19), residues: 708 sheet: -0.94 (0.20), residues: 645 loop : -2.61 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 694 TYR 0.086 0.002 TYR C1141 PHE 0.035 0.002 PHE A 895 TRP 0.063 0.003 TRP B 310 HIS 0.033 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00553 (27441) covalent geometry : angle 1.19211 (37314) SS BOND : bond 0.00943 ( 36) SS BOND : angle 2.25593 ( 72) hydrogen bonds : bond 0.03982 ( 840) hydrogen bonds : angle 5.78877 ( 2241) Misc. bond : bond 0.00249 ( 3) =============================================================================== Job complete usr+sys time: 4747.70 seconds wall clock time: 83 minutes 10.87 seconds (4990.87 seconds total)