Starting phenix.real_space_refine on Sun Nov 17 15:31:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_23766.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_23766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_23766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_23766.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md4_23766/11_2024/7md4_23766.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 9.29, per 1000 atoms: 0.67 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=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.95 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: 6.35 Time building geometry restraints manager: 3.60 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: 1.50 - 2.18: 12 2.18 - 2.86: 4951 2.86 - 3.54: 20471 3.54 - 4.22: 37457 4.22 - 4.90: 59130 Nonbonded interactions: 122021 Sorted by model distance: nonbonded pdb=" NH1 ARG N 702 " pdb=" CE1 TYR A 144 " model vdw 1.500 3.420 nonbonded pdb=" CZ ARG N 702 " pdb=" CE1 TYR A 144 " model vdw 1.651 3.570 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 3.420 ... (remaining 122016 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: 1.120 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.190 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.540 ------------------------------------------------------------------------------- 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 14243 Z= 1.264 Angle : 1.358 17.102 19293 Z= 0.768 Chirality : 0.063 0.304 2097 Planarity : 0.008 0.059 2486 Dihedral : 10.202 69.108 5257 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 19.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.038 0.005 TRP B 551 HIS 0.020 0.004 HIS B 429 PHE 0.053 0.005 PHE B 400 TYR 0.029 0.005 TYR B 579 ARG 0.015 0.002 ARG B 885 *********************** 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 : 1.672 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 553 MET cc_start: 0.9331 (mtt) cc_final: 0.9011 (mmm) REVERT: A 419 LEU cc_start: 0.9285 (tp) cc_final: 0.9044 (tp) REVERT: A 579 TYR cc_start: 0.7688 (m-10) cc_final: 0.7147 (m-80) 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: 0.3334 time to fit residues: 80.8314 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 : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 0.0170 chunk 152 optimal weight: 10.0000 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 HIS B 21 HIS B 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 407 ASN B 452 GLN B 455 ASN ** B 561 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2998 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: