Starting phenix.real_space_refine on Mon Mar 18 19:55:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/03_2024/6nzu_0560_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9466 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 S 58 5.16 5 C 7908 2.51 5 N 2170 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 140": "NH1" <-> "NH2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 246": "OD1" <-> "OD2" Residue "E TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ASP 339": "OD1" <-> "OD2" Residue "E PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "J ASP 167": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} bond proxies already assigned to first conformer: 3180 Chain: "B" Number of atoms: 685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 677 Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "E" Number of atoms: 3139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 402, 3131 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 382} bond proxies already assigned to first conformer: 3180 Chain: "F" Number of atoms: 685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 677 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 547 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "I" Number of atoms: 937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} bond proxies already assigned to first conformer: 946 Chain: "J" Number of atoms: 937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} bond proxies already assigned to first conformer: 946 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4837 SG CYS D 95 40.937 34.759 42.193 1.00 28.53 S ATOM 5154 SG CYS D 138 38.986 35.454 38.852 1.00 36.64 S ATOM 10135 SG CYS H 95 106.818 67.369 42.226 1.00 28.88 S ATOM 10452 SG CYS H 138 108.816 66.663 38.916 1.00 37.27 S Time building chain proxies: 10.98, per 1000 atoms: 0.87 Number of scatterers: 12570 At special positions: 0 Unit cell: (148.782, 103.17, 106.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 4 15.00 O 2428 8.00 N 2170 7.00 C 7908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 95 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 138 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 138 " 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 10 sheets defined 40.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.264A pdb=" N ALA A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 100 through 114 removed outlier: 3.868A pdb=" N ARG A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.919A pdb=" N SER A 162 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.904A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.088A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 315 through 334 removed outlier: 3.592A pdb=" N HIS A 319 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.597A pdb=" N GLU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.831A pdb=" N ARG B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 42 removed outlier: 3.567A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.767A pdb=" N VAL B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 12 through 15 No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 58 through 61 No H-bonds generated for 'chain 'C' and resid 58 through 61' Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.772A pdb=" N TYR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 44 removed outlier: 4.098A pdb=" N HIS D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 3.537A pdb=" N ALA D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.557A pdb=" N LYS D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 152 removed outlier: 3.657A pdb=" N LEU D 136 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS D 137 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 141 " --> pdb=" O CYS D 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 143 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP D 144 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS D 147 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU D 150 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.275A pdb=" N ALA E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.864A pdb=" N ARG E 107 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.915A pdb=" N SER E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.947A pdb=" N ILE E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 298 through 308 removed outlier: 4.091A pdb=" N GLY E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 336 removed outlier: 3.599A pdb=" N HIS E 319 " --> pdb=" O MET E 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 367 No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 399 through 401 No H-bonds generated for 'chain 'E' and resid 399 through 401' Processing helix chain 'E' and resid 416 through 428 removed outlier: 3.613A pdb=" N GLU E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 427 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN E 428 " --> pdb=" O GLU E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.815A pdb=" N ARG F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 42 removed outlier: 3.574A pdb=" N ARG F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.775A pdb=" N VAL F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 66 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 10 No H-bonds generated for 'chain 'G' and resid 7 through 10' Processing helix chain 'G' and resid 12 through 15 No H-bonds generated for 'chain 'G' and resid 12 through 15' Processing helix chain 'G' and resid 37 through 49 Processing helix chain 'G' and resid 58 through 61 No H-bonds generated for 'chain 'G' and resid 58 through 61' Processing helix chain 'G' and resid 66 through 73 removed outlier: 3.772A pdb=" N TYR G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 removed outlier: 4.097A pdb=" N HIS H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 removed outlier: 3.535A pdb=" N ALA H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS H 110 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 119 Processing helix chain 'H' and resid 122 through 128 removed outlier: 3.557A pdb=" N LYS H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 152 removed outlier: 3.656A pdb=" N LEU H 136 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS H 137 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET H 140 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU H 141 " --> pdb=" O CYS H 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 143 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP H 144 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS H 147 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU H 150 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 102 removed outlier: 3.701A pdb=" N GLU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 removed outlier: 3.955A pdb=" N PHE I 109 " --> pdb=" O SER I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 115 No H-bonds generated for 'chain 'I' and resid 113 through 115' Processing helix chain 'I' and resid 182 through 194 removed outlier: 4.053A pdb=" N ALA I 187 " --> pdb=" O HIS I 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA I 193 " --> pdb=" O GLU I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 removed outlier: 3.689A pdb=" N GLU J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 removed outlier: 4.005A pdb=" N PHE J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 115 No H-bonds generated for 'chain 'J' and resid 113 through 115' Processing helix chain 'J' and resid 182 through 194 removed outlier: 4.104A pdb=" N ALA J 187 " --> pdb=" O HIS J 183 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.555A pdb=" N THR A 124 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 172 through 176 removed outlier: 7.556A pdb=" N ILE A 150 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 200 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR A 152 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 353 through 357 Processing sheet with id= D, first strand: chain 'D' and resid 62 through 66 removed outlier: 3.771A pdb=" N ASP D 71 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D 87 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.557A pdb=" N THR E 124 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 172 through 176 removed outlier: 7.557A pdb=" N ILE E 150 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL E 200 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR E 152 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 353 through 357 Processing sheet with id= H, first strand: chain 'H' and resid 62 through 66 removed outlier: 3.770A pdb=" N ASP H 71 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP H 87 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 131 through 133 removed outlier: 3.527A pdb=" N VAL I 144 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 144 through 148 removed outlier: 3.543A pdb=" N VAL J 144 " --> pdb=" O SER J 157 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 946 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: 3.57 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2999 1.33 - 1.45: 2540 1.45 - 1.57: 7145 1.57 - 1.69: 4 1.69 - 1.81: 94 Bond restraints: 12782 Sorted by residual: bond pdb=" C34 8Q1 G 101 " pdb=" N36 8Q1 G 101 " ideal model delta sigma weight residual 1.473 1.325 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C34 8Q1 C 101 " pdb=" N36 8Q1 C 101 " ideal model delta sigma weight residual 1.473 1.325 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C39 8Q1 C 101 " pdb=" N41 8Q1 C 101 " ideal model delta sigma weight residual 1.466 1.337 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C39 8Q1 G 101 " pdb=" N41 8Q1 G 101 " ideal model delta sigma weight residual 1.466 1.337 0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C6 8Q1 G 101 " pdb=" C7 8Q1 G 101 " ideal model delta sigma weight residual 1.577 1.492 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 12777 not shown) Histogram of bond angle deviations from ideal: 96.45 - 103.99: 167 103.99 - 111.52: 5428 111.52 - 119.06: 5098 119.06 - 126.59: 6421 126.59 - 134.13: 158 Bond angle restraints: 17272 Sorted by residual: angle pdb=" C TYR B 28 " pdb=" N ARG B 29 " pdb=" CA ARG B 29 " ideal model delta sigma weight residual 120.54 125.19 -4.65 1.35e+00 5.49e-01 1.19e+01 angle pdb=" N LEU E 449 " pdb=" CA LEU E 449 " pdb=" CB LEU E 449 " ideal model delta sigma weight residual 113.65 108.75 4.90 1.47e+00 4.63e-01 1.11e+01 angle pdb=" C THR E 382 " pdb=" N SER E 383 " pdb=" CA SER E 383 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C1 8Q1 C 101 " pdb=" S44 8Q1 C 101 " pdb=" C43 8Q1 C 101 " ideal model delta sigma weight residual 109.51 100.80 8.71 3.00e+00 1.11e-01 8.44e+00 angle pdb=" C1 8Q1 G 101 " pdb=" S44 8Q1 G 101 " pdb=" C43 8Q1 G 101 " ideal model delta sigma weight residual 109.51 100.80 8.71 3.00e+00 1.11e-01 8.42e+00 ... (remaining 17267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 7506 27.83 - 55.67: 289 55.67 - 83.50: 26 83.50 - 111.33: 1 111.33 - 139.17: 2 Dihedral angle restraints: 7824 sinusoidal: 3192 harmonic: 4632 Sorted by residual: dihedral pdb=" C5A PLP E 501 " pdb=" O4P PLP E 501 " pdb=" P PLP E 501 " pdb=" O1P PLP E 501 " ideal model delta sinusoidal sigma weight residual 76.43 -62.74 139.17 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -61.11 137.54 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" CA ALA J 204 " pdb=" C ALA J 204 " pdb=" N TYR J 205 " pdb=" CA TYR J 205 " ideal model delta harmonic sigma weight residual 180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1218 0.049 - 0.098: 545 0.098 - 0.147: 172 0.147 - 0.196: 12 0.196 - 0.246: 3 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CG LEU E 251 " pdb=" CB LEU E 251 " pdb=" CD1 LEU E 251 " pdb=" CD2 LEU E 251 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 251 " pdb=" CB LEU A 251 " pdb=" CD1 LEU A 251 " pdb=" CD2 LEU A 251 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL A 265 " pdb=" CA VAL A 265 " pdb=" CG1 VAL A 265 " pdb=" CG2 VAL A 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 1947 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 C 101 " 0.048 2.00e-02 2.50e+03 5.10e-02 3.25e+01 pdb=" C39 8Q1 C 101 " -0.021 2.00e-02 2.50e+03 pdb=" C42 8Q1 C 101 " 0.062 2.00e-02 2.50e+03 pdb=" N41 8Q1 C 101 " -0.080 2.00e-02 2.50e+03 pdb=" O40 8Q1 C 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 G 101 " 0.047 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" C39 8Q1 G 101 " -0.021 2.00e-02 2.50e+03 pdb=" C42 8Q1 G 101 " 0.061 2.00e-02 2.50e+03 pdb=" N41 8Q1 G 101 " -0.080 2.00e-02 2.50e+03 pdb=" O40 8Q1 G 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 273 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 274 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 274 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 274 " -0.037 5.00e-02 4.00e+02 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 131 2.63 - 3.19: 11136 3.19 - 3.76: 17501 3.76 - 4.33: 26748 4.33 - 4.90: 44880 Nonbonded interactions: 100396 Sorted by model distance: nonbonded pdb=" O LEU H 52 " pdb=" OD1 ASP H 53 " model vdw 2.057 3.040 nonbonded pdb=" O LEU D 52 " pdb=" OD1 ASP D 53 " model vdw 2.057 3.040 nonbonded pdb=" O VAL H 72 " pdb=" OG1 THR H 92 " model vdw 2.196 2.440 nonbonded pdb=" O PRO H 133 " pdb=" OG SER J 157 " model vdw 2.197 2.440 nonbonded pdb=" O VAL D 72 " pdb=" OG1 THR D 92 " model vdw 2.201 2.440 ... (remaining 100391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 104 or resid 106 through 457 or resid 501)) selection = (chain 'E' and (resid 56 through 104 or resid 106 through 457 or resid 501)) } ncs_group { reference = (chain 'B' and (resid 5 through 70 or resid 72 through 85)) selection = (chain 'F' and (resid 5 through 70 or resid 72 through 85)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 90 through 134 or resid 136 through 207)) selection = (chain 'J' and (resid 90 through 134 or resid 136 through 207)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 2.470 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 43.580 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.130 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:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.014 0.148 12782 Z= 0.875 Angle : 0.885 8.714 17272 Z= 0.443 Chirality : 0.057 0.246 1950 Planarity : 0.005 0.065 2216 Dihedral : 14.457 139.169 4844 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.92 (0.15), residues: 1574 helix: -4.61 (0.09), residues: 682 sheet: -3.15 (0.31), residues: 220 loop : -3.24 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 173 HIS 0.006 0.001 HIS E 230 PHE 0.020 0.002 PHE B 23 TYR 0.015 0.002 TYR D 35 ARG 0.005 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.493 Fit side-chains REVERT: A 119 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7802 (mtm180) REVERT: A 223 SER cc_start: 0.8549 (t) cc_final: 0.8321 (p) REVERT: D 57 LYS cc_start: 0.7620 (tttt) cc_final: 0.7359 (tppt) REVERT: E 119 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7775 (mtm180) REVERT: E 385 SER cc_start: 0.9094 (t) cc_final: 0.8814 (p) REVERT: H 115 GLU cc_start: 0.7184 (pt0) cc_final: 0.6884 (mp0) REVERT: I 198 LEU cc_start: 0.8068 (mm) cc_final: 0.7683 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3429 time to fit residues: 75.0669 Evaluate side-chains 116 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS A 456 GLN D 48 ASN E 429 HIS E 456 GLN I 153 GLN J 151 ASN J 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12782 Z= 0.179 Angle : 0.551 6.186 17272 Z= 0.280 Chirality : 0.044 0.134 1950 Planarity : 0.004 0.052 2216 Dihedral : 7.921 94.723 1786 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.73 % Allowed : 8.36 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.50 (0.17), residues: 1574 helix: -3.15 (0.14), residues: 698 sheet: -2.41 (0.31), residues: 228 loop : -2.82 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 173 HIS 0.004 0.001 HIS H 42 PHE 0.010 0.001 PHE D 93 TYR 0.012 0.001 TYR H 43 ARG 0.003 0.000 ARG F 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.392 Fit side-chains REVERT: A 119 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7708 (mtm180) REVERT: A 272 ARG cc_start: 0.7957 (ttt-90) cc_final: 0.7702 (ttp80) REVERT: A 342 MET cc_start: 0.8208 (ttt) cc_final: 0.7937 (ttt) REVERT: D 57 LYS cc_start: 0.7643 (tttt) cc_final: 0.7370 (tptt) REVERT: E 119 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7722 (mtm180) REVERT: E 342 MET cc_start: 0.8149 (ttt) cc_final: 0.7920 (ttt) REVERT: E 385 SER cc_start: 0.9143 (t) cc_final: 0.8909 (p) REVERT: H 58 ASN cc_start: 0.7997 (p0) cc_final: 0.7797 (p0) REVERT: I 198 LEU cc_start: 0.8115 (mm) cc_final: 0.7640 (mt) REVERT: J 147 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8662 (ptmt) outliers start: 10 outliers final: 5 residues processed: 149 average time/residue: 0.3441 time to fit residues: 67.7716 Evaluate side-chains 129 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain I residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 0.0070 chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 456 GLN E 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12782 Z= 0.207 Angle : 0.529 5.876 17272 Z= 0.265 Chirality : 0.044 0.139 1950 Planarity : 0.004 0.051 2216 Dihedral : 6.870 88.915 1786 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.73 % Allowed : 10.78 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.18), residues: 1574 helix: -2.25 (0.17), residues: 728 sheet: -2.18 (0.30), residues: 242 loop : -2.30 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 173 HIS 0.003 0.001 HIS H 42 PHE 0.009 0.001 PHE F 23 TYR 0.013 0.001 TYR F 28 ARG 0.002 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.359 Fit side-chains REVERT: A 119 ARG cc_start: 0.8256 (mtm180) cc_final: 0.7973 (mtm180) REVERT: A 324 LYS cc_start: 0.7886 (mttm) cc_final: 0.7601 (mtmm) REVERT: A 342 MET cc_start: 0.8365 (ttt) cc_final: 0.8105 (ttt) REVERT: A 364 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: D 57 LYS cc_start: 0.7700 (tttt) cc_final: 0.7423 (tptt) REVERT: E 119 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7874 (mtm180) REVERT: E 220 ARG cc_start: 0.8292 (ttp80) cc_final: 0.8019 (ttp80) REVERT: E 289 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8264 (mtt90) REVERT: E 324 LYS cc_start: 0.7872 (mttm) cc_final: 0.7604 (mtmm) REVERT: E 342 MET cc_start: 0.8322 (ttt) cc_final: 0.8056 (ttt) REVERT: E 364 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6787 (mm-30) REVERT: E 385 SER cc_start: 0.9111 (t) cc_final: 0.8909 (p) REVERT: H 73 MET cc_start: 0.8392 (mtt) cc_final: 0.8163 (mtt) outliers start: 10 outliers final: 6 residues processed: 141 average time/residue: 0.3505 time to fit residues: 65.5434 Evaluate side-chains 130 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN I 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12782 Z= 0.257 Angle : 0.539 5.902 17272 Z= 0.271 Chirality : 0.045 0.147 1950 Planarity : 0.004 0.051 2216 Dihedral : 6.779 89.981 1786 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.17 % Allowed : 11.66 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.08 (0.19), residues: 1574 helix: -1.82 (0.18), residues: 730 sheet: -1.84 (0.31), residues: 246 loop : -2.17 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 173 HIS 0.003 0.001 HIS A 89 PHE 0.011 0.001 PHE F 23 TYR 0.013 0.001 TYR B 28 ARG 0.003 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.517 Fit side-chains REVERT: A 119 ARG cc_start: 0.8273 (mtm180) cc_final: 0.8006 (mtm180) REVERT: A 324 LYS cc_start: 0.7892 (mttm) cc_final: 0.7609 (mtmm) REVERT: A 342 MET cc_start: 0.8530 (ttt) cc_final: 0.8236 (ttt) REVERT: B 44 LYS cc_start: 0.8870 (tttt) cc_final: 0.8356 (ttpp) REVERT: C 39 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: D 57 LYS cc_start: 0.7619 (tttt) cc_final: 0.7371 (tptt) REVERT: E 119 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7865 (mtm180) REVERT: E 324 LYS cc_start: 0.7893 (mttm) cc_final: 0.7611 (mtmm) REVERT: E 342 MET cc_start: 0.8483 (ttt) cc_final: 0.8211 (ttt) REVERT: E 370 LEU cc_start: 0.8611 (mt) cc_final: 0.8317 (mp) REVERT: F 44 LYS cc_start: 0.8902 (tttt) cc_final: 0.8674 (tttt) REVERT: G 39 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: H 73 MET cc_start: 0.8431 (mtt) cc_final: 0.8193 (mtt) REVERT: I 101 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7187 (mt-10) REVERT: I 191 THR cc_start: 0.9009 (m) cc_final: 0.8654 (p) REVERT: J 191 THR cc_start: 0.8916 (m) cc_final: 0.8579 (p) REVERT: J 198 LEU cc_start: 0.8180 (mm) cc_final: 0.7836 (mm) outliers start: 16 outliers final: 11 residues processed: 152 average time/residue: 0.3327 time to fit residues: 67.9033 Evaluate side-chains 146 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 456 GLN D 42 HIS I 151 ASN J 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12782 Z= 0.279 Angle : 0.542 6.027 17272 Z= 0.272 Chirality : 0.045 0.151 1950 Planarity : 0.003 0.049 2216 Dihedral : 6.770 88.415 1786 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.42 % Allowed : 11.14 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.77 (0.19), residues: 1574 helix: -1.56 (0.18), residues: 730 sheet: -1.62 (0.31), residues: 246 loop : -2.06 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 173 HIS 0.003 0.001 HIS E 257 PHE 0.012 0.001 PHE F 23 TYR 0.013 0.002 TYR I 118 ARG 0.004 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.398 Fit side-chains REVERT: A 119 ARG cc_start: 0.8276 (mtm180) cc_final: 0.8024 (mtm180) REVERT: A 289 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8287 (mtt90) REVERT: A 324 LYS cc_start: 0.7892 (mttm) cc_final: 0.7509 (mtmm) REVERT: A 334 MET cc_start: 0.8397 (mtt) cc_final: 0.7824 (mtt) REVERT: A 342 MET cc_start: 0.8633 (ttt) cc_final: 0.8342 (ttt) REVERT: A 364 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: C 39 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: D 57 LYS cc_start: 0.7614 (tttt) cc_final: 0.7305 (tptt) REVERT: E 119 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7875 (mtm180) REVERT: E 324 LYS cc_start: 0.7924 (mttm) cc_final: 0.7614 (mtmm) REVERT: E 342 MET cc_start: 0.8533 (ttt) cc_final: 0.8244 (ttt) REVERT: E 364 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: G 39 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: H 73 MET cc_start: 0.8440 (mtt) cc_final: 0.8200 (mtt) REVERT: I 191 THR cc_start: 0.9042 (m) cc_final: 0.8682 (p) REVERT: J 191 THR cc_start: 0.8993 (m) cc_final: 0.8655 (p) outliers start: 33 outliers final: 21 residues processed: 166 average time/residue: 0.3191 time to fit residues: 71.3699 Evaluate side-chains 161 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN E 428 GLN I 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12782 Z= 0.125 Angle : 0.464 5.722 17272 Z= 0.237 Chirality : 0.042 0.126 1950 Planarity : 0.003 0.047 2216 Dihedral : 6.395 86.722 1786 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.76 % Allowed : 11.73 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.20), residues: 1574 helix: -1.02 (0.19), residues: 726 sheet: -1.30 (0.32), residues: 238 loop : -1.76 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 173 HIS 0.002 0.000 HIS H 42 PHE 0.007 0.001 PHE F 40 TYR 0.012 0.001 TYR H 43 ARG 0.002 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.511 Fit side-chains REVERT: A 119 ARG cc_start: 0.8229 (mtm180) cc_final: 0.7994 (mtm180) REVERT: A 289 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8264 (mtt90) REVERT: A 324 LYS cc_start: 0.7750 (mttm) cc_final: 0.7488 (mtmm) REVERT: A 334 MET cc_start: 0.8293 (mtt) cc_final: 0.7653 (mtt) REVERT: A 342 MET cc_start: 0.8496 (ttt) cc_final: 0.8172 (ttt) REVERT: C 39 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: D 57 LYS cc_start: 0.7545 (tttt) cc_final: 0.7338 (tptt) REVERT: E 119 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7864 (mtm180) REVERT: E 324 LYS cc_start: 0.7869 (mttm) cc_final: 0.7586 (mtmm) REVERT: E 334 MET cc_start: 0.8303 (mtt) cc_final: 0.7992 (mtt) REVERT: E 342 MET cc_start: 0.8422 (ttt) cc_final: 0.8069 (ttt) REVERT: E 364 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6441 (mm-30) REVERT: G 39 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: H 73 MET cc_start: 0.8408 (mtt) cc_final: 0.8205 (mtt) REVERT: I 191 THR cc_start: 0.9010 (m) cc_final: 0.8643 (p) REVERT: J 101 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7273 (mt-10) REVERT: J 191 THR cc_start: 0.8984 (m) cc_final: 0.8650 (p) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.3314 time to fit residues: 72.5385 Evaluate side-chains 154 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN E 428 GLN I 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12782 Z= 0.239 Angle : 0.516 5.720 17272 Z= 0.260 Chirality : 0.044 0.145 1950 Planarity : 0.003 0.052 2216 Dihedral : 6.571 88.756 1786 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.83 % Allowed : 11.58 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.20), residues: 1574 helix: -0.95 (0.19), residues: 726 sheet: -1.30 (0.32), residues: 242 loop : -1.80 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 173 HIS 0.003 0.001 HIS H 42 PHE 0.011 0.001 PHE F 23 TYR 0.020 0.002 TYR D 43 ARG 0.003 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.380 Fit side-chains REVERT: A 119 ARG cc_start: 0.8260 (mtm180) cc_final: 0.8004 (mtm180) REVERT: A 289 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.8231 (mtt90) REVERT: A 324 LYS cc_start: 0.7800 (mttm) cc_final: 0.7527 (mtmm) REVERT: A 334 MET cc_start: 0.8395 (mtt) cc_final: 0.7827 (mtt) REVERT: A 342 MET cc_start: 0.8629 (ttt) cc_final: 0.8331 (ttt) REVERT: C 39 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: D 57 LYS cc_start: 0.7563 (tttt) cc_final: 0.7304 (tptt) REVERT: E 119 ARG cc_start: 0.8214 (mtm180) cc_final: 0.8002 (mtm180) REVERT: E 324 LYS cc_start: 0.7907 (mttm) cc_final: 0.7612 (mtmm) REVERT: E 342 MET cc_start: 0.8518 (ttt) cc_final: 0.8212 (ttt) REVERT: E 364 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6779 (mm-30) REVERT: G 39 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: H 73 MET cc_start: 0.8439 (mtt) cc_final: 0.8234 (mtt) REVERT: I 191 THR cc_start: 0.9023 (m) cc_final: 0.8663 (p) REVERT: J 101 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7225 (mt-10) REVERT: J 191 THR cc_start: 0.8997 (m) cc_final: 0.8636 (p) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 0.3287 time to fit residues: 69.5627 Evaluate side-chains 157 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN E 456 GLN I 151 ASN J 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12782 Z= 0.196 Angle : 0.491 5.318 17272 Z= 0.249 Chirality : 0.043 0.134 1950 Planarity : 0.003 0.048 2216 Dihedral : 6.540 88.527 1786 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.83 % Allowed : 12.17 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.20), residues: 1574 helix: -0.80 (0.19), residues: 730 sheet: -1.25 (0.32), residues: 246 loop : -1.68 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 173 HIS 0.003 0.001 HIS H 42 PHE 0.009 0.001 PHE F 23 TYR 0.020 0.001 TYR H 43 ARG 0.002 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.499 Fit side-chains REVERT: A 119 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7987 (mtm180) REVERT: A 289 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8234 (mtt90) REVERT: A 324 LYS cc_start: 0.7792 (mttm) cc_final: 0.7533 (mtmm) REVERT: A 334 MET cc_start: 0.8398 (mtt) cc_final: 0.7866 (mtt) REVERT: A 342 MET cc_start: 0.8579 (ttt) cc_final: 0.8258 (ttt) REVERT: C 39 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: D 57 LYS cc_start: 0.7520 (tttt) cc_final: 0.7261 (tptt) REVERT: E 119 ARG cc_start: 0.8218 (mtm180) cc_final: 0.8004 (mtm180) REVERT: E 324 LYS cc_start: 0.7923 (mttm) cc_final: 0.7595 (mtmm) REVERT: E 334 MET cc_start: 0.8323 (mtt) cc_final: 0.7757 (mtt) REVERT: E 342 MET cc_start: 0.8489 (ttt) cc_final: 0.8147 (ttt) REVERT: E 364 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6780 (mm-30) REVERT: G 39 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: I 101 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7206 (mt-10) REVERT: I 168 TRP cc_start: 0.8565 (t-100) cc_final: 0.8285 (t-100) REVERT: I 191 THR cc_start: 0.9029 (m) cc_final: 0.8641 (p) REVERT: J 101 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7212 (mt-10) REVERT: J 191 THR cc_start: 0.9013 (m) cc_final: 0.8667 (p) outliers start: 25 outliers final: 19 residues processed: 154 average time/residue: 0.3430 time to fit residues: 70.7969 Evaluate side-chains 157 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN I 151 ASN J 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12782 Z= 0.264 Angle : 0.529 6.178 17272 Z= 0.267 Chirality : 0.045 0.148 1950 Planarity : 0.003 0.050 2216 Dihedral : 6.667 88.167 1786 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.76 % Allowed : 12.32 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.20), residues: 1574 helix: -0.77 (0.19), residues: 728 sheet: -1.20 (0.31), residues: 264 loop : -1.83 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 108 HIS 0.003 0.001 HIS D 42 PHE 0.012 0.001 PHE F 23 TYR 0.020 0.002 TYR D 43 ARG 0.004 0.000 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.488 Fit side-chains REVERT: A 119 ARG cc_start: 0.8257 (mtm180) cc_final: 0.8046 (mtm180) REVERT: A 289 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8246 (mtt90) REVERT: A 324 LYS cc_start: 0.7825 (mttm) cc_final: 0.7542 (mtmm) REVERT: A 334 MET cc_start: 0.8407 (mtt) cc_final: 0.7910 (mtt) REVERT: A 342 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (ttt) REVERT: C 39 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: D 57 LYS cc_start: 0.7531 (tttt) cc_final: 0.7256 (tptt) REVERT: E 119 ARG cc_start: 0.8229 (mtm180) cc_final: 0.8003 (mtm180) REVERT: E 324 LYS cc_start: 0.7909 (mttm) cc_final: 0.7608 (mtmm) REVERT: E 334 MET cc_start: 0.8328 (mtt) cc_final: 0.7801 (mtt) REVERT: E 342 MET cc_start: 0.8531 (ttt) cc_final: 0.8241 (ttt) REVERT: E 364 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: G 39 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: I 168 TRP cc_start: 0.8597 (t-100) cc_final: 0.8302 (t-100) REVERT: I 191 THR cc_start: 0.9025 (m) cc_final: 0.8650 (p) REVERT: J 191 THR cc_start: 0.9003 (m) cc_final: 0.8629 (p) REVERT: J 192 LYS cc_start: 0.8268 (tmmt) cc_final: 0.8000 (tttm) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.3190 time to fit residues: 66.6813 Evaluate side-chains 159 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 155 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 98 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN E 428 GLN E 456 GLN I 151 ASN J 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12782 Z= 0.108 Angle : 0.457 6.420 17272 Z= 0.234 Chirality : 0.041 0.123 1950 Planarity : 0.003 0.044 2216 Dihedral : 6.219 87.371 1786 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.95 % Allowed : 13.64 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.21), residues: 1574 helix: -0.33 (0.20), residues: 730 sheet: -1.12 (0.32), residues: 248 loop : -1.46 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 108 HIS 0.002 0.000 HIS A 230 PHE 0.009 0.001 PHE B 40 TYR 0.013 0.001 TYR D 43 ARG 0.002 0.000 ARG E 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.510 Fit side-chains REVERT: A 324 LYS cc_start: 0.7794 (mttm) cc_final: 0.7513 (mtmm) REVERT: A 334 MET cc_start: 0.8355 (mtt) cc_final: 0.7772 (mtt) REVERT: A 342 MET cc_start: 0.8444 (ttt) cc_final: 0.8116 (ttt) REVERT: C 39 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: D 57 LYS cc_start: 0.7551 (tttt) cc_final: 0.7202 (ttpp) REVERT: E 324 LYS cc_start: 0.7860 (mttm) cc_final: 0.7575 (mtmm) REVERT: E 334 MET cc_start: 0.8294 (mtt) cc_final: 0.7677 (mtt) REVERT: E 342 MET cc_start: 0.8383 (ttt) cc_final: 0.8043 (ttt) REVERT: E 364 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: G 39 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: I 101 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7212 (mt-10) REVERT: I 191 THR cc_start: 0.8991 (m) cc_final: 0.8594 (p) REVERT: J 101 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7224 (mt-10) REVERT: J 191 THR cc_start: 0.8968 (m) cc_final: 0.8594 (p) outliers start: 13 outliers final: 8 residues processed: 158 average time/residue: 0.3177 time to fit residues: 68.0163 Evaluate side-chains 148 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN I 151 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.109539 restraints weight = 35965.233| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.24 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12782 Z= 0.117 Angle : 0.458 6.063 17272 Z= 0.233 Chirality : 0.042 0.124 1950 Planarity : 0.003 0.048 2216 Dihedral : 6.145 86.043 1786 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.88 % Allowed : 13.86 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.21), residues: 1574 helix: -0.03 (0.20), residues: 728 sheet: -1.05 (0.33), residues: 248 loop : -1.40 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 108 HIS 0.002 0.000 HIS H 42 PHE 0.008 0.001 PHE B 40 TYR 0.014 0.001 TYR D 43 ARG 0.003 0.000 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.33 seconds wall clock time: 46 minutes 12.47 seconds (2772.47 seconds total)