Starting phenix.real_space_refine on Wed Mar 4 13:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7md4_23766/03_2026/7md4_23766.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 111 5.16 5 C 8844 2.51 5 N 2379 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13913 Number of models: 1 Model: "" Number of chains: 12 Chain: "N" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 192 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "M" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6290 Classifications: {'peptide': 778} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 735} Chain breaks: 5 Chain: "A" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5871 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 686} Chain breaks: 5 Chain: "U" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "V" Number of atoms: 226 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 221 Chain: "S" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "T" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 213 Chain: "Q" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13913 At special positions: 0 Unit cell: (162.24, 139.36, 145.6, 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 111 16.00 O 2579 8.00 N 2379 7.00 C 8844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.01 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.04 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.05 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.00 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.00 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.02 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.04 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=1.99 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.01 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.05 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.00 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.00 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.05 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.04 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=1.98 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 11 " distance=2.03 Simple disulfide: pdb=" SG CYS U 7 " - pdb=" SG CYS V 7 " distance=2.04 Simple disulfide: pdb=" SG CYS U 20 " - pdb=" SG CYS V 19 " distance=2.01 Simple disulfide: pdb=" SG CYS S 6 " - pdb=" SG CYS S 11 " distance=2.03 Simple disulfide: pdb=" SG CYS S 7 " - pdb=" SG CYS T 7 " distance=2.05 Simple disulfide: pdb=" SG CYS S 20 " - pdb=" SG CYS T 19 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 11 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 7 " - pdb=" SG CYS R 7 " distance=2.03 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 11 " distance=2.03 Simple disulfide: pdb=" SG CYS O 7 " - pdb=" SG CYS P 7 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 407.7 milliseconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 34 sheets defined 17.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'N' and resid 694 through 714 removed outlier: 3.532A pdb=" N SER N 700 " --> pdb=" O LEU N 696 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE N 705 " --> pdb=" O PHE N 701 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS N 710 " --> pdb=" O GLU N 706 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN N 711 " --> pdb=" O ASP N 707 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL N 712 " --> pdb=" O TYR N 708 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL N 713 " --> pdb=" O LEU N 709 " (cutoff:3.500A) Processing helix chain 'M' and resid 706 through 714 removed outlier: 3.800A pdb=" N HIS M 710 " --> pdb=" O GLU M 706 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN M 711 " --> pdb=" O ASP M 707 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 712 " --> pdb=" O TYR M 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL M 713 " --> pdb=" O LEU M 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.561A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.657A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.795A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.518A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.938A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 863 through 870 Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.562A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.655A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.795A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.517A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.938A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 12 through 18 removed outlier: 3.620A pdb=" N ASN U 18 " --> pdb=" O TYR U 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 20 removed outlier: 3.659A pdb=" N HIS V 10 " --> pdb=" O LEU V 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU V 11 " --> pdb=" O CYS V 7 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU V 13 " --> pdb=" O SER V 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 12 through 18 removed outlier: 3.621A pdb=" N ASN S 18 " --> pdb=" O TYR S 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 20 removed outlier: 3.590A pdb=" N HIS T 10 " --> pdb=" O LEU T 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU T 11 " --> pdb=" O CYS T 7 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU T 13 " --> pdb=" O SER T 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 12 through 18 removed outlier: 3.619A pdb=" N ASN Q 18 " --> pdb=" O TYR Q 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 12 through 18 removed outlier: 3.621A pdb=" N ASN O 18 " --> pdb=" O TYR O 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 20 removed outlier: 3.806A pdb=" N VAL R 12 " --> pdb=" O GLY R 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 removed outlier: 3.725A pdb=" N GLU P 13 " --> pdb=" O SER P 9 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 11 removed outlier: 7.014A pdb=" N GLU B 6 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU B 30 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 82 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 11 removed outlier: 7.014A pdb=" N GLU B 6 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU B 30 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 64 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER B 116 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'B' and resid 320 through 321 removed outlier: 6.115A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AA9, first strand: chain 'B' and resid 398 through 403 removed outlier: 5.305A pdb=" N TYR B 398 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE B 427 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE B 400 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 473 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB3, first strand: chain 'B' and resid 532 through 534 Processing sheet with id=AB4, first strand: chain 'B' and resid 602 through 604 Processing sheet with id=AB5, first strand: chain 'B' and resid 759 through 763 Processing sheet with id=AB6, first strand: chain 'B' and resid 818 through 821 Processing sheet with id=AB7, first strand: chain 'B' and resid 860 through 862 removed outlier: 3.692A pdb=" N LEU B 844 " --> pdb=" O THR B 889 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 850 " --> pdb=" O SER B 883 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 860 through 862 removed outlier: 3.692A pdb=" N LEU B 844 " --> pdb=" O THR B 889 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 850 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 882 " --> pdb=" O PHE B 903 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 903 " --> pdb=" O TYR B 882 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 8 through 11 removed outlier: 6.510A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 8 through 11 removed outlier: 6.510A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER A 116 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AC3, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AC4, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AC6, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.115A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AC8, first strand: chain 'A' and resid 398 through 403 removed outlier: 5.306A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 471 through 473 Processing sheet with id=AD1, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AD2, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AD3, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AD4, first strand: chain 'A' and resid 759 through 763 Processing sheet with id=AD5, first strand: chain 'A' and resid 818 through 821 Processing sheet with id=AD6, first strand: chain 'A' and resid 860 through 862 removed outlier: 3.692A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 889 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 850 " --> pdb=" O SER A 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 860 through 862 removed outlier: 3.692A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 889 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 850 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 882 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 903 " --> pdb=" O TYR A 882 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 864 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: 2.55 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.38: 5697 1.38 - 1.66: 8408 1.66 - 1.94: 134 1.94 - 2.22: 2 2.22 - 2.50: 2 Bond restraints: 14243 Sorted by residual: bond pdb=" C THR A 593 " pdb=" N ASN A 594 " ideal model delta sigma weight residual 1.326 2.500 -1.174 1.66e-02 3.63e+03 5.00e+03 bond pdb=" C THR B 593 " pdb=" N ASN B 594 " ideal model delta sigma weight residual 1.326 2.499 -1.173 1.66e-02 3.63e+03 4.99e+03 bond pdb=" C ASP B 591 " pdb=" N ALA B 592 " ideal model delta sigma weight residual 1.332 2.195 -0.863 1.40e-02 5.10e+03 3.80e+03 bond pdb=" C ASP A 591 " pdb=" N ALA A 592 " ideal model delta sigma weight residual 1.332 2.194 -0.862 1.40e-02 5.10e+03 3.79e+03 bond pdb=" C PHE N 705 " pdb=" N GLU N 706 " ideal model delta sigma weight residual 1.335 1.719 -0.384 1.35e-02 5.49e+03 8.09e+02 ... (remaining 14238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 18751 3.42 - 6.84: 467 6.84 - 10.26: 62 10.26 - 13.68: 10 13.68 - 17.10: 3 Bond angle restraints: 19293 Sorted by residual: angle pdb=" O PHE N 705 " pdb=" C PHE N 705 " pdb=" N GLU N 706 " ideal model delta sigma weight residual 122.59 138.92 -16.33 1.33e+00 5.65e-01 1.51e+02 angle pdb=" C PHE N 705 " pdb=" N GLU N 706 " pdb=" CA GLU N 706 " ideal model delta sigma weight residual 120.60 104.20 16.40 1.60e+00 3.91e-01 1.05e+02 angle pdb=" CA PHE N 705 " pdb=" C PHE N 705 " pdb=" N GLU N 706 " ideal model delta sigma weight residual 116.84 99.74 17.10 1.71e+00 3.42e-01 1.00e+02 angle pdb=" N GLU N 697 " pdb=" CA GLU N 697 " pdb=" C GLU N 697 " ideal model delta sigma weight residual 112.45 103.52 8.93 1.39e+00 5.18e-01 4.13e+01 angle pdb=" O THR N 704 " pdb=" C THR N 704 " pdb=" N PHE N 705 " ideal model delta sigma weight residual 122.15 129.39 -7.24 1.14e+00 7.69e-01 4.03e+01 ... (remaining 19288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 7939 14.91 - 29.81: 547 29.81 - 44.72: 96 44.72 - 59.62: 17 59.62 - 74.53: 14 Dihedral angle restraints: 8613 sinusoidal: 3586 harmonic: 5027 Sorted by residual: dihedral pdb=" CB CYS U 7 " pdb=" SG CYS U 7 " pdb=" SG CYS V 7 " pdb=" CB CYS V 7 " ideal model delta sinusoidal sigma weight residual 93.00 163.48 -70.48 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS S 7 " pdb=" SG CYS S 7 " pdb=" SG CYS T 7 " pdb=" CB CYS T 7 " ideal model delta sinusoidal sigma weight residual 93.00 160.46 -67.46 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA ARG B 851 " pdb=" C ARG B 851 " pdb=" N TYR B 852 " pdb=" CA TYR B 852 " ideal model delta harmonic sigma weight residual 180.00 145.54 34.46 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 8610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1475 0.061 - 0.121: 510 0.121 - 0.182: 99 0.182 - 0.243: 5 0.243 - 0.304: 8 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CB ILE B 195 " pdb=" CA ILE B 195 " pdb=" CG1 ILE B 195 " pdb=" CG2 ILE B 195 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CG LEU A 552 " pdb=" CB LEU A 552 " pdb=" CD1 LEU A 552 " pdb=" CD2 LEU A 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2094 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE N 705 " 0.016 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PHE N 705 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE N 705 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU N 706 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS V 10 " -0.028 2.00e-02 2.50e+03 2.85e-02 1.22e+01 pdb=" CG AHIS V 10 " 0.061 2.00e-02 2.50e+03 pdb=" ND1AHIS V 10 " -0.007 2.00e-02 2.50e+03 pdb=" CD2AHIS V 10 " -0.014 2.00e-02 2.50e+03 pdb=" CE1AHIS V 10 " -0.009 2.00e-02 2.50e+03 pdb=" NE2AHIS V 10 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 400 " 0.033 2.00e-02 2.50e+03 2.43e-02 1.04e+01 pdb=" CG PHE B 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 400 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 400 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 400 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 400 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 400 " 0.006 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 142 2.47 - 3.08: 9322 3.08 - 3.69: 23744 3.69 - 4.29: 34766 4.29 - 4.90: 54043 Nonbonded interactions: 122017 Sorted by model distance: nonbonded pdb=" OE2 GLU A 120 " pdb=" OH TYR A 144 " model vdw 1.866 3.040 nonbonded pdb=" OE2 GLU B 120 " pdb=" OH TYR B 144 " model vdw 1.866 3.040 nonbonded pdb=" NH2 ARG N 702 " pdb=" CE1 TYR A 144 " model vdw 1.937 2.736 nonbonded pdb=" OE1 GLU B 120 " pdb=" CE2 TYR B 144 " model vdw 2.064 3.340 nonbonded pdb=" OE1 GLU A 120 " pdb=" CE2 TYR A 144 " model vdw 2.064 3.340 ... (remaining 122012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 7 through 147 or resid 196 through 304 or resid 318 throug \ h 909)) } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = (chain 'P' and (resid 5 through 9 or resid 11 through 27)) selection = (chain 'R' and (resid 5 through 9 or resid 11 through 27)) selection = (chain 'T' and (resid 5 through 9 or resid 11 through 27)) } 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=0.50 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 : 0.020 1.174 14282 Z= 1.249 Angle : 1.367 17.102 19369 Z= 0.771 Chirality : 0.063 0.304 2097 Planarity : 0.008 0.059 2486 Dihedral : 10.202 69.108 5257 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.41 % Favored : 90.11 % Rotamer: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.18), residues: 1668 helix: -3.24 (0.25), residues: 178 sheet: -1.81 (0.28), residues: 309 loop : -2.01 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 885 TYR 0.029 0.005 TYR B 579 PHE 0.053 0.005 PHE B 400 TRP 0.038 0.005 TRP B 551 HIS 0.020 0.004 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.02049 (14243) covalent geometry : angle 1.35764 (19293) SS BOND : bond 0.01855 ( 38) SS BOND : angle 2.85405 ( 76) hydrogen bonds : bond 0.32583 ( 326) hydrogen bonds : angle 11.97072 ( 864) Misc. bond : bond 0.07036 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.7718 (ttp) cc_final: 0.7511 (tmm) REVERT: B 419 LEU cc_start: 0.9121 (tp) cc_final: 0.8815 (tp) REVERT: B 504 MET cc_start: 0.6250 (mtp) cc_final: 0.6011 (mtt) REVERT: B 553 MET cc_start: 0.9331 (mtt) cc_final: 0.8980 (mmm) REVERT: A 419 LEU cc_start: 0.9285 (tp) cc_final: 0.9043 (tp) REVERT: U 19 TYR cc_start: 0.5765 (m-80) cc_final: 0.5307 (m-80) REVERT: V 22 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8288 (mtp180) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1336 time to fit residues: 32.6462 Evaluate side-chains 80 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN B 21 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 405 ASN B 407 ASN B 452 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN A 21 HIS A 111 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 405 ASN A 407 ASN A 452 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN V 4 GLN ** V 10 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 HIS B Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.073918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.057109 restraints weight = 159078.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.058891 restraints weight = 88065.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.060025 restraints weight = 57874.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.060721 restraints weight = 43619.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.061135 restraints weight = 36484.057| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14282 Z= 0.166 Angle : 0.742 8.244 19369 Z= 0.393 Chirality : 0.048 0.225 2097 Planarity : 0.005 0.086 2486 Dihedral : 7.610 81.702 1885 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.19), residues: 1676 helix: -2.18 (0.28), residues: 217 sheet: -1.62 (0.27), residues: 328 loop : -1.81 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 372 TYR 0.026 0.002 TYR N 708 PHE 0.026 0.002 PHE A 248 TRP 0.025 0.002 TRP B 551 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00342 (14243) covalent geometry : angle 0.74075 (19293) SS BOND : bond 0.00534 ( 38) SS BOND : angle 1.00446 ( 76) hydrogen bonds : bond 0.05176 ( 326) hydrogen bonds : angle 8.79712 ( 864) Misc. bond : bond 0.00404 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 VAL cc_start: 0.8246 (t) cc_final: 0.8044 (t) REVERT: B 56 MET cc_start: 0.8575 (ttp) cc_final: 0.8058 (tmm) REVERT: B 419 LEU cc_start: 0.7657 (tp) cc_final: 0.7225 (tp) REVERT: B 499 ASP cc_start: 0.8171 (m-30) cc_final: 0.7932 (m-30) REVERT: B 504 MET cc_start: 0.8276 (mtp) cc_final: 0.8032 (mtm) REVERT: A 409 ARG cc_start: 0.6616 (mtp180) cc_final: 0.5295 (mtt-85) REVERT: A 412 TRP cc_start: 0.8045 (m-90) cc_final: 0.7723 (m-90) REVERT: A 797 VAL cc_start: 0.8843 (m) cc_final: 0.8599 (p) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1116 time to fit residues: 19.9589 Evaluate side-chains 77 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 548 HIS ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 HIS P 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.069730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.052730 restraints weight = 163366.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.054282 restraints weight = 88529.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.055044 restraints weight = 58885.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.055874 restraints weight = 46121.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.056254 restraints weight = 38976.432| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14282 Z= 0.264 Angle : 0.852 14.997 19369 Z= 0.432 Chirality : 0.049 0.210 2097 Planarity : 0.006 0.077 2486 Dihedral : 7.442 86.171 1885 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.43 % Favored : 90.45 % Rotamer: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.20), residues: 1676 helix: -1.68 (0.31), residues: 216 sheet: -1.69 (0.27), residues: 350 loop : -1.67 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 554 TYR 0.037 0.003 TYR B 430 PHE 0.021 0.003 PHE B 565 TRP 0.040 0.003 TRP A 551 HIS 0.009 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00559 (14243) covalent geometry : angle 0.84971 (19293) SS BOND : bond 0.00409 ( 38) SS BOND : angle 1.23504 ( 76) hydrogen bonds : bond 0.05185 ( 326) hydrogen bonds : angle 8.31977 ( 864) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.8989 (ttp) cc_final: 0.8686 (tmm) REVERT: B 499 ASP cc_start: 0.8520 (m-30) cc_final: 0.8055 (m-30) REVERT: A 409 ARG cc_start: 0.6940 (mtp180) cc_final: 0.5728 (ttt90) REVERT: A 412 TRP cc_start: 0.8670 (m-90) cc_final: 0.8386 (m-90) REVERT: A 499 ASP cc_start: 0.8570 (m-30) cc_final: 0.8196 (m-30) REVERT: A 535 ASP cc_start: 0.9141 (p0) cc_final: 0.8881 (p0) REVERT: A 797 VAL cc_start: 0.8997 (m) cc_final: 0.8768 (p) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0995 time to fit residues: 14.1090 Evaluate side-chains 67 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 27 optimal weight: 40.0000 chunk 144 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN B 826 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN A 826 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.070364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.053958 restraints weight = 161549.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.055660 restraints weight = 86330.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.056716 restraints weight = 55897.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.057304 restraints weight = 42516.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.057799 restraints weight = 35991.741| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14282 Z= 0.137 Angle : 0.655 14.561 19369 Z= 0.336 Chirality : 0.046 0.224 2097 Planarity : 0.004 0.076 2486 Dihedral : 6.888 85.105 1885 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.20), residues: 1676 helix: -1.25 (0.31), residues: 229 sheet: -1.43 (0.27), residues: 338 loop : -1.62 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 554 TYR 0.022 0.002 TYR U 19 PHE 0.014 0.002 PHE B 565 TRP 0.019 0.002 TRP A 551 HIS 0.011 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00281 (14243) covalent geometry : angle 0.65452 (19293) SS BOND : bond 0.00225 ( 38) SS BOND : angle 0.76992 ( 76) hydrogen bonds : bond 0.03806 ( 326) hydrogen bonds : angle 7.55635 ( 864) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 MET cc_start: 0.8997 (ttp) cc_final: 0.8495 (tmm) REVERT: B 412 TRP cc_start: 0.8083 (m-90) cc_final: 0.7371 (m-90) REVERT: A 409 ARG cc_start: 0.6875 (mtp180) cc_final: 0.5710 (mtt-85) REVERT: A 412 TRP cc_start: 0.8530 (m-90) cc_final: 0.8323 (m-90) REVERT: A 499 ASP cc_start: 0.8481 (m-30) cc_final: 0.8055 (m-30) REVERT: A 535 ASP cc_start: 0.9078 (p0) cc_final: 0.8836 (p0) REVERT: A 797 VAL cc_start: 0.8955 (m) cc_final: 0.8716 (p) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0959 time to fit residues: 14.1113 Evaluate side-chains 74 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 10 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.066297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.049681 restraints weight = 162755.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.051239 restraints weight = 85929.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.051974 restraints weight = 57049.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.052737 restraints weight = 44960.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.053213 restraints weight = 38492.619| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14282 Z= 0.270 Angle : 0.837 18.274 19369 Z= 0.422 Chirality : 0.049 0.234 2097 Planarity : 0.006 0.070 2486 Dihedral : 7.142 85.263 1885 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.20), residues: 1676 helix: -1.25 (0.31), residues: 230 sheet: -1.65 (0.27), residues: 350 loop : -1.66 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 539 TYR 0.038 0.003 TYR B 430 PHE 0.028 0.002 PHE A 248 TRP 0.042 0.003 TRP A 551 HIS 0.010 0.002 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00565 (14243) covalent geometry : angle 0.83446 (19293) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.25336 ( 76) hydrogen bonds : bond 0.04788 ( 326) hydrogen bonds : angle 7.98733 ( 864) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 419 LEU cc_start: 0.8629 (tp) cc_final: 0.8207 (tp) REVERT: B 474 LYS cc_start: 0.8284 (tptp) cc_final: 0.8027 (tptp) REVERT: A 409 ARG cc_start: 0.7025 (mtp180) cc_final: 0.6001 (mtt-85) REVERT: A 499 ASP cc_start: 0.8759 (m-30) cc_final: 0.8266 (m-30) REVERT: A 535 ASP cc_start: 0.9156 (p0) cc_final: 0.8886 (p0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1033 time to fit residues: 13.6484 Evaluate side-chains 58 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 161 optimal weight: 40.0000 chunk 129 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.070178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.053224 restraints weight = 158079.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.054922 restraints weight = 82936.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056035 restraints weight = 53682.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.056724 restraints weight = 40352.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.057009 restraints weight = 33661.117| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14282 Z= 0.126 Angle : 0.651 17.115 19369 Z= 0.331 Chirality : 0.046 0.258 2097 Planarity : 0.004 0.065 2486 Dihedral : 6.583 84.743 1885 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.94 % Favored : 92.00 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1676 helix: -1.05 (0.31), residues: 229 sheet: -1.42 (0.27), residues: 344 loop : -1.51 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 554 TYR 0.020 0.002 TYR U 14 PHE 0.020 0.002 PHE A 248 TRP 0.021 0.002 TRP B 551 HIS 0.009 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00268 (14243) covalent geometry : angle 0.65062 (19293) SS BOND : bond 0.00233 ( 38) SS BOND : angle 0.76584 ( 76) hydrogen bonds : bond 0.03715 ( 326) hydrogen bonds : angle 7.37848 ( 864) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 412 TRP cc_start: 0.8089 (m-90) cc_final: 0.7497 (m-90) REVERT: B 616 LYS cc_start: 0.9424 (mmpt) cc_final: 0.9199 (mmtm) REVERT: A 409 ARG cc_start: 0.6837 (mtp180) cc_final: 0.5872 (mtt-85) REVERT: A 419 LEU cc_start: 0.8399 (tp) cc_final: 0.8197 (tp) REVERT: A 465 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 499 ASP cc_start: 0.8045 (m-30) cc_final: 0.7748 (m-30) REVERT: A 535 ASP cc_start: 0.9148 (p0) cc_final: 0.8926 (p0) REVERT: P 17 LEU cc_start: 0.9442 (mt) cc_final: 0.9217 (pp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0956 time to fit residues: 13.5323 Evaluate side-chains 66 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.069524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.052565 restraints weight = 158724.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.054267 restraints weight = 82591.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.055242 restraints weight = 53979.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.056021 restraints weight = 40999.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.056438 restraints weight = 34215.242| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14282 Z= 0.131 Angle : 0.643 15.070 19369 Z= 0.323 Chirality : 0.045 0.252 2097 Planarity : 0.004 0.060 2486 Dihedral : 6.352 82.371 1885 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.06 % Allowed : 1.21 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.20), residues: 1676 helix: -0.98 (0.32), residues: 231 sheet: -1.35 (0.27), residues: 347 loop : -1.47 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 554 TYR 0.021 0.002 TYR A 845 PHE 0.015 0.001 PHE A 427 TRP 0.019 0.002 TRP A 414 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00283 (14243) covalent geometry : angle 0.64227 (19293) SS BOND : bond 0.00217 ( 38) SS BOND : angle 0.72376 ( 76) hydrogen bonds : bond 0.03609 ( 326) hydrogen bonds : angle 7.22433 ( 864) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 TRP cc_start: 0.8445 (m-90) cc_final: 0.7435 (m-90) REVERT: B 616 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9156 (mmtm) REVERT: A 465 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 499 ASP cc_start: 0.8148 (m-30) cc_final: 0.7840 (m-30) REVERT: A 535 ASP cc_start: 0.9167 (p0) cc_final: 0.8924 (p0) REVERT: P 17 LEU cc_start: 0.9412 (mt) cc_final: 0.9156 (pp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0879 time to fit residues: 11.6855 Evaluate side-chains 60 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 163 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.068057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.051224 restraints weight = 160010.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.052899 restraints weight = 83877.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.053994 restraints weight = 54858.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.054639 restraints weight = 41207.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.055030 restraints weight = 34696.604| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14282 Z= 0.172 Angle : 0.695 17.548 19369 Z= 0.349 Chirality : 0.046 0.276 2097 Planarity : 0.005 0.060 2486 Dihedral : 6.341 82.886 1885 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.21), residues: 1676 helix: -0.84 (0.32), residues: 232 sheet: -1.39 (0.27), residues: 355 loop : -1.49 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 554 TYR 0.021 0.002 TYR B 430 PHE 0.014 0.002 PHE B 427 TRP 0.024 0.002 TRP A 551 HIS 0.013 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00359 (14243) covalent geometry : angle 0.69452 (19293) SS BOND : bond 0.00242 ( 38) SS BOND : angle 0.79878 ( 76) hydrogen bonds : bond 0.03825 ( 326) hydrogen bonds : angle 7.32332 ( 864) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: B 419 LEU cc_start: 0.8490 (tp) cc_final: 0.8014 (tp) REVERT: B 474 LYS cc_start: 0.8183 (tptp) cc_final: 0.7962 (tptp) REVERT: B 616 LYS cc_start: 0.9492 (mmpt) cc_final: 0.9211 (mmtm) REVERT: A 419 LEU cc_start: 0.8674 (tp) cc_final: 0.8433 (tp) REVERT: A 465 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 499 ASP cc_start: 0.8182 (m-30) cc_final: 0.7853 (m-30) REVERT: P 17 LEU cc_start: 0.9440 (mt) cc_final: 0.9183 (pp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0906 time to fit residues: 12.0448 Evaluate side-chains 64 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.066957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.050362 restraints weight = 156807.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.052035 restraints weight = 82764.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.053120 restraints weight = 54170.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.053690 restraints weight = 41142.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.054069 restraints weight = 34643.917| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14282 Z= 0.182 Angle : 0.707 19.943 19369 Z= 0.352 Chirality : 0.045 0.186 2097 Planarity : 0.005 0.058 2486 Dihedral : 6.332 81.838 1885 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1676 helix: -1.03 (0.33), residues: 220 sheet: -1.49 (0.27), residues: 349 loop : -1.48 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 554 TYR 0.046 0.002 TYR N 708 PHE 0.013 0.002 PHE B 565 TRP 0.029 0.002 TRP B 412 HIS 0.007 0.001 HIS P 5 Details of bonding type rmsd covalent geometry : bond 0.00384 (14243) covalent geometry : angle 0.70631 (19293) SS BOND : bond 0.00267 ( 38) SS BOND : angle 0.83766 ( 76) hydrogen bonds : bond 0.03920 ( 326) hydrogen bonds : angle 7.41600 ( 864) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.9466 (tp) cc_final: 0.9238 (tp) REVERT: B 419 LEU cc_start: 0.8516 (tp) cc_final: 0.8242 (tp) REVERT: B 474 LYS cc_start: 0.8280 (tptp) cc_final: 0.8036 (tptp) REVERT: A 419 LEU cc_start: 0.8673 (tp) cc_final: 0.8208 (tt) REVERT: A 499 ASP cc_start: 0.8234 (m-30) cc_final: 0.7922 (m-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0838 time to fit residues: 10.7018 Evaluate side-chains 57 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 40 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 710 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.068100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.051490 restraints weight = 154470.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.053167 restraints weight = 80170.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.054233 restraints weight = 52627.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.054834 restraints weight = 39559.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.055243 restraints weight = 33290.405| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14282 Z= 0.123 Angle : 0.634 18.650 19369 Z= 0.318 Chirality : 0.045 0.193 2097 Planarity : 0.004 0.058 2486 Dihedral : 6.064 81.832 1885 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.21), residues: 1676 helix: -0.90 (0.34), residues: 220 sheet: -1.29 (0.27), residues: 353 loop : -1.46 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.021 0.002 TYR U 14 PHE 0.015 0.001 PHE N 705 TRP 0.023 0.002 TRP B 412 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00263 (14243) covalent geometry : angle 0.63419 (19293) SS BOND : bond 0.00178 ( 38) SS BOND : angle 0.69442 ( 76) hydrogen bonds : bond 0.03611 ( 326) hydrogen bonds : angle 7.18766 ( 864) Misc. bond : bond 0.00065 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.9460 (tp) cc_final: 0.9040 (tp) REVERT: B 419 LEU cc_start: 0.8398 (tp) cc_final: 0.7793 (tt) REVERT: B 474 LYS cc_start: 0.8141 (tptp) cc_final: 0.7901 (tptp) REVERT: A 419 LEU cc_start: 0.8619 (tp) cc_final: 0.8191 (tt) REVERT: A 435 CYS cc_start: 0.4165 (t) cc_final: 0.3821 (t) REVERT: A 465 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7786 (tm-30) REVERT: A 499 ASP cc_start: 0.8158 (m-30) cc_final: 0.7840 (m-30) REVERT: P 17 LEU cc_start: 0.9424 (mt) cc_final: 0.9152 (pp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0851 time to fit residues: 11.8797 Evaluate side-chains 66 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.067130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.050725 restraints weight = 155111.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.052420 restraints weight = 80864.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.053485 restraints weight = 52682.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.054104 restraints weight = 39709.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.054512 restraints weight = 33162.615| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14282 Z= 0.129 Angle : 0.636 16.865 19369 Z= 0.318 Chirality : 0.045 0.195 2097 Planarity : 0.004 0.057 2486 Dihedral : 5.889 79.841 1885 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.21), residues: 1676 helix: -0.83 (0.34), residues: 220 sheet: -1.22 (0.27), residues: 353 loop : -1.42 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 554 TYR 0.020 0.002 TYR U 14 PHE 0.014 0.001 PHE N 705 TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00276 (14243) covalent geometry : angle 0.63571 (19293) SS BOND : bond 0.00195 ( 38) SS BOND : angle 0.66511 ( 76) hydrogen bonds : bond 0.03468 ( 326) hydrogen bonds : angle 7.00854 ( 864) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.91 seconds wall clock time: 66 minutes 5.86 seconds (3965.86 seconds total)