Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 03:48:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_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_0560/04_2023/6nzu_0560_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzu_0560/04_2023/6nzu_0560_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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-1.21rc1-4938/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: 10.93, 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: 5.31 Conformation dependent library (CDL) restraints added in 3.1 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: 1.19 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: 3.11 Time building geometry restraints manager: 5.42 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: 285 55.67 - 83.50: 26 83.50 - 111.33: 1 111.33 - 139.17: 2 Dihedral angle restraints: 7820 sinusoidal: 3188 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 7817 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 2.960 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.650 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.090 ------------------------------------------------------------------------------- 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 : 14.419 139.169 4840 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 % 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 *********************** 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 : 1.446 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3467 time to fit residues: 76.0252 Evaluate side-chains 115 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0362 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12782 Z= 0.173 Angle : 0.550 5.939 17272 Z= 0.281 Chirality : 0.044 0.136 1950 Planarity : 0.004 0.052 2216 Dihedral : 7.637 93.775 1782 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 0.66 % 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: -4.48 (0.17), residues: 1574 helix: -3.12 (0.14), residues: 698 sheet: -2.32 (0.31), residues: 224 loop : -2.85 (0.20), residues: 652 *********************** 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 150 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.547 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 147 average time/residue: 0.3688 time to fit residues: 71.0002 Evaluate side-chains 124 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1259 time to fit residues: 2.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.0270 chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 12782 Z= 0.129 Angle : 0.482 5.250 17272 Z= 0.244 Chirality : 0.042 0.197 1950 Planarity : 0.003 0.054 2216 Dihedral : 6.399 86.042 1782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.15 % 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: -3.35 (0.19), residues: 1574 helix: -2.08 (0.17), residues: 710 sheet: -1.96 (0.31), residues: 232 loop : -2.30 (0.21), residues: 632 *********************** 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 129 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.506 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.3502 time to fit residues: 61.0170 Evaluate side-chains 115 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1085 time to fit residues: 2.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.0670 chunk 150 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 153 GLN J 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2864 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= 0.240 Angle : 0.535 6.261 17272 Z= 0.268 Chirality : 0.045 0.150 1950 Planarity : 0.003 0.057 2216 Dihedral : 6.471 88.305 1782 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.88 % 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: -2.96 (0.19), residues: 1574 helix: -1.75 (0.18), residues: 730 sheet: -1.78 (0.31), residues: 240 loop : -2.08 (0.22), residues: 604 *********************** 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 151 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.550 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.3461 time to fit residues: 68.6063 Evaluate side-chains 137 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1573 time to fit residues: 4.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN I 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12782 Z= 0.233 Angle : 0.524 6.972 17272 Z= 0.262 Chirality : 0.044 0.151 1950 Planarity : 0.003 0.052 2216 Dihedral : 6.334 89.031 1782 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.32 % 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: -2.64 (0.20), residues: 1574 helix: -1.50 (0.18), residues: 730 sheet: -1.58 (0.31), residues: 240 loop : -1.92 (0.22), residues: 604 *********************** 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 152 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.487 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 149 average time/residue: 0.3455 time to fit residues: 69.1454 Evaluate side-chains 136 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1148 time to fit residues: 3.6133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.0070 chunk 150 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 overall best weight: 1.2180 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12782 Z= 0.166 Angle : 0.487 6.370 17272 Z= 0.247 Chirality : 0.043 0.130 1950 Planarity : 0.003 0.050 2216 Dihedral : 6.128 87.036 1782 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.73 % 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: -2.27 (0.20), residues: 1574 helix: -1.18 (0.19), residues: 730 sheet: -1.44 (0.32), residues: 242 loop : -1.72 (0.23), residues: 602 *********************** 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 146 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.650 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 143 average time/residue: 0.3613 time to fit residues: 69.1660 Evaluate side-chains 136 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1193 time to fit residues: 3.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 12782 Z= 0.132 Angle : 0.465 6.543 17272 Z= 0.237 Chirality : 0.042 0.127 1950 Planarity : 0.003 0.048 2216 Dihedral : 5.897 84.405 1782 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.51 % 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: -1.87 (0.20), residues: 1574 helix: -0.82 (0.19), residues: 730 sheet: -1.27 (0.32), residues: 240 loop : -1.55 (0.24), residues: 604 *********************** 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 145 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.478 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 142 average time/residue: 0.3575 time to fit residues: 67.9553 Evaluate side-chains 137 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1241 time to fit residues: 2.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.3513 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= 0.283 Angle : 0.537 6.032 17272 Z= 0.270 Chirality : 0.045 0.154 1950 Planarity : 0.003 0.053 2216 Dihedral : 6.276 88.038 1782 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.51 % 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: -2.04 (0.20), residues: 1574 helix: -0.90 (0.19), residues: 730 sheet: -1.41 (0.31), residues: 252 loop : -1.70 (0.23), residues: 592 *********************** 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 149 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 1.473 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 147 average time/residue: 0.3420 time to fit residues: 67.6721 Evaluate side-chains 141 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1116 time to fit residues: 2.8734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0030 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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: 0.8192 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 12782 Z= 0.164 Angle : 0.482 6.299 17272 Z= 0.245 Chirality : 0.043 0.128 1950 Planarity : 0.003 0.047 2216 Dihedral : 6.023 86.509 1782 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.22 % 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: -1.76 (0.21), residues: 1574 helix: -0.67 (0.19), residues: 730 sheet: -1.25 (0.32), residues: 252 loop : -1.58 (0.24), residues: 592 *********************** 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 141 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.569 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 141 average time/residue: 0.3526 time to fit residues: 67.0493 Evaluate side-chains 138 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1109 time to fit residues: 2.6941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 0.0870 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 chunk 98 optimal weight: 6.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 12782 Z= 0.120 Angle : 0.459 6.193 17272 Z= 0.234 Chirality : 0.042 0.124 1950 Planarity : 0.003 0.047 2216 Dihedral : 5.726 84.462 1782 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % 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: -1.42 (0.21), residues: 1574 helix: -0.36 (0.20), residues: 732 sheet: -1.13 (0.32), residues: 248 loop : -1.41 (0.24), residues: 594 ********************** 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 136 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3428 time to fit residues: 63.5061 Evaluate side-chains 131 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105800 restraints weight = 36136.961| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.20 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3673 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= 0.261 Angle : 0.532 6.223 17272 Z= 0.268 Chirality : 0.045 0.148 1950 Planarity : 0.003 0.052 2216 Dihedral : 6.185 89.002 1782 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.07 % 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: -1.59 (0.21), residues: 1574 helix: -0.49 (0.20), residues: 728 sheet: -1.18 (0.32), residues: 252 loop : -1.54 (0.24), residues: 594 =============================================================================== Job complete usr+sys time: 2367.05 seconds wall clock time: 44 minutes 19.61 seconds (2659.61 seconds total)