Starting phenix.real_space_refine on Mon Dec 30 21:28:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7md4_23766/12_2024/7md4_23766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7md4_23766/12_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/cci-nas-00/data/ceres_data/7md4_23766/12_2024/7md4_23766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7md4_23766/12_2024/7md4_23766.map" model { file = "/net/cci-nas-00/data/ceres_data/7md4_23766/12_2024/7md4_23766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7md4_23766/12_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-5532/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: 8.62, per 1000 atoms: 0.62 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: 3.61 Conformation dependent library (CDL) restraints added in 1.9 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: 2.02 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: 5.48 Time building geometry restraints manager: 4.05 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: 1.370 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.480 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- 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= 1.174 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 : 1.866 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 : 1.710 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: 0.3253 time to fit residues: 79.2188 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 : 1.949 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN 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: 0.6849 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14243 Z= 0.294 Angle : 0.799 9.225 19293 Z= 0.420 Chirality : 0.048 0.213 2097 Planarity : 0.006 0.095 2486 Dihedral : 7.733 82.363 1885 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.79 (0.19), residues: 1676 helix: -2.34 (0.28), residues: 222 sheet: -1.79 (0.27), residues: 333 loop : -1.84 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 551 HIS 0.007 0.001 HIS A 429 PHE 0.028 0.002 PHE A 248 TYR 0.027 0.002 TYR N 708 ARG 0.008 0.001 ARG B 554 *********************** 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 108 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.745 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: B 28 VAL cc_start: 0.8426 (t) cc_final: 0.8196 (p) REVERT: B 56 MET cc_start: 0.8217 (ttp) cc_final: 0.7900 (tmm) REVERT: B 419 LEU cc_start: 0.9226 (tp) cc_final: 0.8932 (tp) REVERT: B 551 TRP cc_start: 0.8588 (t-100) cc_final: 0.8292 (t-100) REVERT: B 553 MET cc_start: 0.9400 (mtt) cc_final: 0.9132 (mmm) REVERT: A 409 ARG cc_start: 0.5750 (mtp180) cc_final: 0.5060 (mtt-85) REVERT: A 419 LEU cc_start: 0.9254 (tp) cc_final: 0.9005 (tp) REVERT: A 553 MET cc_start: 0.9534 (mmp) cc_final: 0.9076 (mmp) REVERT: A 584 ASP cc_start: 0.9110 (t0) cc_final: 0.8871 (p0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3136 time to fit residues: 50.5559 Evaluate side-chains 75 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 0.0470 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 0.0060 overall best weight: 2.0100 ------------------------------------------------------------------------------- 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 HIS A 209 HIS A 455 ASN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 10 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14243 Z= 0.210 Angle : 0.666 12.863 19293 Z= 0.344 Chirality : 0.046 0.257 2097 Planarity : 0.005 0.081 2486 Dihedral : 7.010 82.838 1885 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.05 % Favored : 91.83 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.19 (0.20), residues: 1676 helix: -1.35 (0.31), residues: 218 sheet: -1.35 (0.27), residues: 333 loop : -1.57 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 551 HIS 0.005 0.001 HIS A 440 PHE 0.014 0.002 PHE A 248 TYR 0.020 0.002 TYR N 708 ARG 0.008 0.001 ARG A 135 *********************** 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 104 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.872 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: 0.8356 (t) cc_final: 0.7933 (t) REVERT: B 56 MET cc_start: 0.8484 (ttp) cc_final: 0.8083 (tmm) REVERT: B 419 LEU cc_start: 0.9173 (tp) cc_final: 0.8952 (tp) REVERT: B 499 ASP cc_start: 0.9033 (m-30) cc_final: 0.8715 (t0) REVERT: B 501 LEU cc_start: 0.9256 (mm) cc_final: 0.8982 (mm) REVERT: B 553 MET cc_start: 0.9524 (mtt) cc_final: 0.9297 (mmm) REVERT: B 584 ASP cc_start: 0.9182 (t0) cc_final: 0.8957 (p0) REVERT: A 329 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9346 (mm-30) REVERT: A 385 LEU cc_start: 0.9469 (tp) cc_final: 0.9206 (mp) REVERT: A 409 ARG cc_start: 0.5816 (mtp180) cc_final: 0.5122 (ttt90) REVERT: A 419 LEU cc_start: 0.9182 (tp) cc_final: 0.8887 (tp) REVERT: A 553 MET cc_start: 0.9543 (mmp) cc_final: 0.9207 (mmp) REVERT: A 579 TYR cc_start: 0.7545 (m-80) cc_final: 0.7316 (m-80) REVERT: A 584 ASP cc_start: 0.9200 (t0) cc_final: 0.8994 (p0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2723 time to fit residues: 43.9127 Evaluate side-chains 73 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 16 optimal weight: 40.0000 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 80 optimal weight: 40.0000 chunk 145 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 561 GLN ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 561 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** V 10 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14243 Z= 0.143 Angle : 0.608 11.877 19293 Z= 0.312 Chirality : 0.046 0.294 2097 Planarity : 0.004 0.072 2486 Dihedral : 6.573 82.515 1885 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.07 (0.20), residues: 1676 helix: -1.05 (0.32), residues: 230 sheet: -1.22 (0.27), residues: 345 loop : -1.54 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 551 HIS 0.007 0.001 HIS B 199 PHE 0.012 0.001 PHE N 705 TYR 0.016 0.001 TYR N 708 ARG 0.004 0.000 ARG A 554 *********************** 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 98 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 VAL cc_start: 0.8216 (t) cc_final: 0.7714 (t) REVERT: B 56 MET cc_start: 0.8505 (ttp) cc_final: 0.8025 (tmm) REVERT: B 412 TRP cc_start: 0.8678 (m-90) cc_final: 0.7999 (m-90) REVERT: B 419 LEU cc_start: 0.9134 (tp) cc_final: 0.8868 (tp) REVERT: B 465 GLN cc_start: 0.7302 (tm-30) cc_final: 0.7031 (tm-30) REVERT: B 499 ASP cc_start: 0.9072 (m-30) cc_final: 0.8756 (t0) REVERT: B 501 LEU cc_start: 0.9334 (mm) cc_final: 0.9091 (mm) REVERT: B 553 MET cc_start: 0.9563 (mtt) cc_final: 0.9237 (mmm) REVERT: A 329 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9303 (mm-30) REVERT: A 385 LEU cc_start: 0.9479 (tp) cc_final: 0.9203 (mp) REVERT: A 409 ARG cc_start: 0.5768 (mtp180) cc_final: 0.5151 (ttt90) REVERT: A 419 LEU cc_start: 0.9204 (tp) cc_final: 0.8913 (tp) REVERT: A 553 MET cc_start: 0.9544 (mmp) cc_final: 0.9272 (mmp) REVERT: A 579 TYR cc_start: 0.7441 (m-80) cc_final: 0.7188 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2675 time to fit residues: 40.8611 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 : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14243 Z= 0.180 Angle : 0.615 12.361 19293 Z= 0.314 Chirality : 0.045 0.246 2097 Planarity : 0.004 0.066 2486 Dihedral : 6.367 79.565 1885 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.06 % Allowed : 1.47 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.20), residues: 1676 helix: -0.81 (0.32), residues: 230 sheet: -1.11 (0.27), residues: 345 loop : -1.46 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 551 HIS 0.005 0.001 HIS B 199 PHE 0.027 0.001 PHE A 248 TYR 0.018 0.001 TYR A 430 ARG 0.005 0.000 ARG A 554 *********************** 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 97 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 VAL cc_start: 0.8316 (t) cc_final: 0.8061 (p) REVERT: B 56 MET cc_start: 0.8579 (ttp) cc_final: 0.8214 (tmm) REVERT: B 385 LEU cc_start: 0.9367 (tp) cc_final: 0.9054 (mp) REVERT: B 419 LEU cc_start: 0.9186 (tp) cc_final: 0.8868 (tp) REVERT: B 465 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 499 ASP cc_start: 0.9107 (m-30) cc_final: 0.8811 (t0) REVERT: B 553 MET cc_start: 0.9576 (mtt) cc_final: 0.9190 (mmm) REVERT: A 329 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9282 (mm-30) REVERT: A 409 ARG cc_start: 0.5750 (mtp180) cc_final: 0.5131 (ttt90) REVERT: A 419 LEU cc_start: 0.9238 (tp) cc_final: 0.8999 (tp) REVERT: A 499 ASP cc_start: 0.8990 (m-30) cc_final: 0.8752 (m-30) REVERT: A 553 MET cc_start: 0.9559 (mmp) cc_final: 0.9194 (mmm) REVERT: A 579 TYR cc_start: 0.7435 (m-80) cc_final: 0.7178 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2498 time to fit residues: 37.8320 Evaluate side-chains 73 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 0.0170 chunk 85 optimal weight: 9.9990 overall best weight: 2.8622 ------------------------------------------------------------------------------- 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN ** B 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN T 10 HIS B Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14243 Z= 0.225 Angle : 0.648 13.873 19293 Z= 0.331 Chirality : 0.045 0.217 2097 Planarity : 0.004 0.060 2486 Dihedral : 6.247 72.098 1885 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % 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 : 0.00 % 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: -1.82 (0.20), residues: 1676 helix: -0.60 (0.32), residues: 232 sheet: -1.07 (0.27), residues: 347 loop : -1.43 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 412 HIS 0.005 0.001 HIS A 417 PHE 0.017 0.002 PHE A 248 TYR 0.023 0.002 TYR B 430 ARG 0.007 0.001 ARG B 554 *********************** 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 89 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 VAL cc_start: 0.8356 (t) cc_final: 0.8050 (p) REVERT: B 56 MET cc_start: 0.8698 (ttp) cc_final: 0.8331 (tmm) REVERT: B 412 TRP cc_start: 0.8330 (m-90) cc_final: 0.7988 (m-90) REVERT: B 419 LEU cc_start: 0.9244 (tp) cc_final: 0.8758 (tp) REVERT: B 499 ASP cc_start: 0.9092 (m-30) cc_final: 0.8795 (t0) REVERT: A 329 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9231 (mm-30) REVERT: A 409 ARG cc_start: 0.5923 (mtp180) cc_final: 0.5378 (ttt90) REVERT: A 419 LEU cc_start: 0.9339 (tp) cc_final: 0.9069 (tp) REVERT: A 499 ASP cc_start: 0.8827 (m-30) cc_final: 0.8620 (t0) REVERT: A 553 MET cc_start: 0.9535 (mmp) cc_final: 0.9210 (mmm) REVERT: A 579 TYR cc_start: 0.7550 (m-80) cc_final: 0.7247 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2464 time to fit residues: 35.7888 Evaluate side-chains 71 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14243 Z= 0.246 Angle : 0.688 15.382 19293 Z= 0.344 Chirality : 0.046 0.233 2097 Planarity : 0.005 0.066 2486 Dihedral : 6.246 66.221 1885 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.59 % Favored : 91.35 % Rotamer: Outliers : 0.06 % Allowed : 1.09 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.81 (0.20), residues: 1676 helix: -0.63 (0.32), residues: 232 sheet: -1.07 (0.28), residues: 338 loop : -1.42 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 414 HIS 0.006 0.001 HIS A 417 PHE 0.018 0.002 PHE A 427 TYR 0.030 0.002 TYR N 708 ARG 0.008 0.001 ARG B 554 *********************** 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 86 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 GLN cc_start: 0.8400 (tp40) cc_final: 0.8162 (tp40) REVERT: B 419 LEU cc_start: 0.9358 (tp) cc_final: 0.9077 (tp) REVERT: B 499 ASP cc_start: 0.9108 (m-30) cc_final: 0.8823 (t0) REVERT: A 329 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9095 (mm-30) REVERT: A 409 ARG cc_start: 0.6059 (mtp180) cc_final: 0.5496 (mtt-85) REVERT: A 419 LEU cc_start: 0.9437 (tp) cc_final: 0.9206 (tp) REVERT: A 499 ASP cc_start: 0.8877 (m-30) cc_final: 0.8646 (t0) REVERT: A 553 MET cc_start: 0.9518 (mmp) cc_final: 0.9137 (mmm) REVERT: A 579 TYR cc_start: 0.7678 (m-80) cc_final: 0.7439 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2538 time to fit residues: 34.6535 Evaluate side-chains 61 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14243 Z= 0.240 Angle : 0.677 17.751 19293 Z= 0.340 Chirality : 0.045 0.210 2097 Planarity : 0.004 0.059 2486 Dihedral : 6.147 61.203 1885 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % 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 (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: -1.87 (0.21), residues: 1676 helix: -0.65 (0.33), residues: 232 sheet: -1.27 (0.27), residues: 346 loop : -1.40 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 551 HIS 0.006 0.001 HIS A 417 PHE 0.015 0.002 PHE N 705 TYR 0.020 0.002 TYR B 492 ARG 0.005 0.001 ARG A 372 *********************** 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 85 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.9017 (m-30) cc_final: 0.8715 (t0) REVERT: A 409 ARG cc_start: 0.6089 (mtp180) cc_final: 0.5559 (mtt-85) REVERT: A 419 LEU cc_start: 0.9477 (tp) cc_final: 0.9239 (tp) REVERT: A 435 CYS cc_start: 0.7952 (t) cc_final: 0.6959 (t) REVERT: A 499 ASP cc_start: 0.8864 (m-30) cc_final: 0.8632 (t0) REVERT: A 553 MET cc_start: 0.9497 (mmp) cc_final: 0.9125 (mmm) REVERT: A 579 TYR cc_start: 0.7828 (m-80) cc_final: 0.7560 (m-80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2243 time to fit residues: 31.0454 Evaluate side-chains 59 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 280 HIS B 455 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14243 Z= 0.182 Angle : 0.631 16.563 19293 Z= 0.317 Chirality : 0.045 0.234 2097 Planarity : 0.004 0.073 2486 Dihedral : 5.933 56.539 1885 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.29 % Favored : 91.65 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.86 (0.21), residues: 1676 helix: -0.70 (0.32), residues: 238 sheet: -1.21 (0.28), residues: 346 loop : -1.41 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 412 HIS 0.004 0.001 HIS B 440 PHE 0.013 0.001 PHE N 705 TYR 0.037 0.002 TYR N 708 ARG 0.011 0.000 ARG A 554 *********************** 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 84 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 ASP cc_start: 0.9001 (m-30) cc_final: 0.8720 (t0) REVERT: A 409 ARG cc_start: 0.5942 (mtp180) cc_final: 0.5415 (mtt-85) REVERT: A 419 LEU cc_start: 0.9480 (tp) cc_final: 0.9269 (tp) REVERT: A 435 CYS cc_start: 0.7858 (t) cc_final: 0.6714 (t) REVERT: A 553 MET cc_start: 0.9456 (mmp) cc_final: 0.9203 (mmm) REVERT: A 579 TYR cc_start: 0.7776 (m-80) cc_final: 0.7543 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2524 time to fit residues: 34.5083 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 : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 110 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14243 Z= 0.145 Angle : 0.604 14.107 19293 Z= 0.304 Chirality : 0.045 0.230 2097 Planarity : 0.004 0.057 2486 Dihedral : 5.587 50.498 1885 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.67 (0.21), residues: 1676 helix: -0.55 (0.33), residues: 231 sheet: -1.02 (0.28), residues: 352 loop : -1.29 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 412 HIS 0.005 0.001 HIS B 429 PHE 0.012 0.001 PHE N 705 TYR 0.026 0.001 TYR N 708 ARG 0.012 0.000 ARG A 554 ********************** 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 89 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 TRP cc_start: 0.8341 (m-90) cc_final: 0.8048 (m-90) REVERT: B 499 ASP cc_start: 0.9010 (m-30) cc_final: 0.8688 (t0) REVERT: B 501 LEU cc_start: 0.9364 (mm) cc_final: 0.9160 (mm) REVERT: B 553 MET cc_start: 0.9174 (mtt) cc_final: 0.8958 (mtp) REVERT: A 409 ARG cc_start: 0.5705 (mtp180) cc_final: 0.5071 (mtt-85) REVERT: A 499 ASP cc_start: 0.8797 (m-30) cc_final: 0.8565 (t0) REVERT: A 579 TYR cc_start: 0.7665 (m-80) cc_final: 0.7383 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2442 time to fit residues: 34.6052 Evaluate side-chains 72 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.068626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.052092 restraints weight = 159558.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.053805 restraints weight = 82537.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.054829 restraints weight = 53241.187| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14243 Z= 0.176 Angle : 0.607 13.325 19293 Z= 0.306 Chirality : 0.044 0.227 2097 Planarity : 0.004 0.056 2486 Dihedral : 5.490 45.239 1885 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.62 (0.21), residues: 1676 helix: -0.39 (0.34), residues: 232 sheet: -1.03 (0.28), residues: 346 loop : -1.27 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 412 HIS 0.005 0.001 HIS R 10 PHE 0.012 0.001 PHE B 565 TYR 0.026 0.002 TYR N 708 ARG 0.007 0.000 ARG A 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.66 seconds wall clock time: 53 minutes 9.89 seconds (3189.89 seconds total)