Starting phenix.real_space_refine on Sun Aug 24 12:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.map" model { file = "/net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nzu_0560/08_2025/6nzu_0560.cif" } 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 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. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.39, per 1000 atoms: 0.43 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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... Secondary structure from input PDB file: 74 helices and 8 sheets defined 47.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.264A pdb=" N ALA A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 99 through 115 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 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 156 through 167 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) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.904A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.088A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.021A pdb=" N GLN A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 337 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) removed outlier: 3.709A pdb=" N SER A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.848A pdb=" N ALA A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.820A pdb=" N VAL A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) 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) removed outlier: 3.569A pdb=" N HIS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 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) Processing helix chain 'B' and resid 25 through 43 removed outlier: 3.567A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 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 6 through 11 removed outlier: 3.917A pdb=" N LYS C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 11' Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.876A pdb=" N THR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.954A pdb=" N GLU C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 removed outlier: 3.772A pdb=" N TYR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 45 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 95 through 109 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) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.503A pdb=" N ILE D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) 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) removed outlier: 3.893A pdb=" N LEU D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 153 removed outlier: 4.163A pdb=" N ALA D 142 " --> pdb=" O CYS D 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.502A pdb=" N LEU E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 99 through 115 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 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 156 through 167 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) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 215 through 225 removed outlier: 3.947A pdb=" N ILE E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 297 through 309 removed outlier: 4.091A pdb=" N GLY E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 314 removed outlier: 4.047A pdb=" N GLN E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 337 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 363 through 368 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.902A pdb=" N ALA E 402 " --> pdb=" O GLU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 426 removed outlier: 3.792A pdb=" N VAL E 419 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 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) Processing helix chain 'F' and resid 25 through 43 removed outlier: 3.574A pdb=" N ARG F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 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 6 through 11 removed outlier: 3.918A pdb=" N LYS G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE G 11 " --> pdb=" O ARG G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 11' Processing helix chain 'G' and resid 11 through 16 Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.877A pdb=" N THR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.954A pdb=" N GLU G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.772A pdb=" N TYR G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 45 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 95 through 109 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) Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 115 through 120 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.503A pdb=" N ILE H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) 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) removed outlier: 3.893A pdb=" N LEU H 129 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 135 Processing helix chain 'H' and resid 136 through 153 removed outlier: 4.163A pdb=" N ALA H 142 " --> pdb=" O CYS H 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 103 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 103 through 111 removed outlier: 3.955A pdb=" N PHE I 109 " --> pdb=" O SER I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.908A pdb=" N ASP I 115 " --> pdb=" O ASP I 112 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS I 116 " --> pdb=" O LEU I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 116' Processing helix chain 'I' and resid 181 through 195 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 91 through 103 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 103 through 111 removed outlier: 4.005A pdb=" N PHE J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 3.900A pdb=" N ASP J 115 " --> pdb=" O ASP J 112 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS J 116 " --> pdb=" O LEU J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 116' Processing helix chain 'J' and resid 181 through 195 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=AA1, 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) removed outlier: 6.651A pdb=" N PHE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N SER A 253 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR A 231 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N SER A 255 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N HIS A 230 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 200 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP A 232 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N SER A 201 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 150 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 149 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU A 176 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 151 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342 Processing sheet with id=AA3, 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: 6.683A pdb=" N LYS D 74 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D 90 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 76 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 88 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN D 78 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AA4, 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) removed outlier: 6.657A pdb=" N PHE E 229 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N SER E 253 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 231 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N SER E 255 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS E 230 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL E 200 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP E 232 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N HIS E 148 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N SER E 201 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 150 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU E 149 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR E 151 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 340 through 342 Processing sheet with id=AA6, 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: 6.682A pdb=" N LYS H 74 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE H 90 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN H 76 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA H 88 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN H 78 " --> pdb=" O VAL H 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 131 through 135 removed outlier: 3.527A pdb=" N VAL I 144 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 131 through 132 removed outlier: 3.543A pdb=" N VAL J 144 " --> pdb=" O SER J 157 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.44 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=" O27 8Q1 G 101 " pdb=" P24 8Q1 G 101 " ideal model delta sigma weight residual 1.678 1.609 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O27 8Q1 C 101 " pdb=" P24 8Q1 C 101 " ideal model delta sigma weight residual 1.678 1.609 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C2 PLP A 501 " pdb=" N1 PLP A 501 " ideal model delta sigma weight residual 1.380 1.328 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" C2 PLP E 501 " pdb=" N1 PLP E 501 " ideal model delta sigma weight residual 1.380 1.328 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" CG1 ILE A 268 " pdb=" CD1 ILE A 268 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.78e+00 ... (remaining 12777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 15605 1.29 - 2.58: 1323 2.58 - 3.87: 232 3.87 - 5.15: 85 5.15 - 6.44: 27 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=" CA ARG B 29 " pdb=" C ARG B 29 " pdb=" O ARG B 29 " ideal model delta sigma weight residual 120.90 117.97 2.93 1.07e+00 8.73e-01 7.47e+00 angle pdb=" C GLU A 362 " pdb=" N GLY A 363 " pdb=" CA GLY A 363 " ideal model delta sigma weight residual 121.41 126.66 -5.25 1.96e+00 2.60e-01 7.16e+00 ... (remaining 17267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 7531 28.11 - 56.22: 272 56.22 - 84.32: 23 84.32 - 112.43: 2 112.43 - 140.54: 10 Dihedral angle restraints: 7838 sinusoidal: 3206 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 7835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1218 0.049 - 0.098: 547 0.098 - 0.147: 170 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: 129 2.63 - 3.19: 11105 3.19 - 3.76: 17423 3.76 - 4.33: 26542 4.33 - 4.90: 44845 Nonbonded interactions: 100044 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 3.040 nonbonded pdb=" O PRO H 133 " pdb=" OG SER J 157 " model vdw 2.197 3.040 nonbonded pdb=" O VAL D 72 " pdb=" OG1 THR D 92 " model vdw 2.201 3.040 ... (remaining 100039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 104 or resid 106 through 501)) selection = (chain 'E' and (resid 56 through 104 or resid 106 through 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.390 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- 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 : 0.018 0.901 12791 Z= 0.990 Angle : 0.857 6.443 17272 Z= 0.437 Chirality : 0.057 0.246 1950 Planarity : 0.005 0.065 2216 Dihedral : 15.220 140.538 4858 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG F 14 TYR 0.015 0.002 TYR D 35 PHE 0.020 0.002 PHE B 23 TRP 0.006 0.001 TRP I 173 HIS 0.006 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.01311 (12782) covalent geometry : angle 0.85711 (17272) hydrogen bonds : bond 0.33122 ( 430) hydrogen bonds : angle 11.05944 ( 1222) metal coordination : bond 0.53484 ( 4) Misc. bond : bond 0.40479 ( 5) *********************** 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 to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.386 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: 0.1444 time to fit residues: 31.8597 Evaluate side-chains 116 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 149 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 429 HIS A 456 GLN D 48 ASN E 156 HIS E 429 HIS I 153 GLN J 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.117813 restraints weight = 34820.797| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.00 r_work: 0.2720 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12791 Z= 0.116 Angle : 0.573 8.364 17272 Z= 0.293 Chirality : 0.044 0.136 1950 Planarity : 0.005 0.051 2216 Dihedral : 9.852 134.935 1800 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.81 % Allowed : 8.06 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.17), residues: 1574 helix: -2.87 (0.15), residues: 702 sheet: -2.43 (0.31), residues: 232 loop : -2.62 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 289 TYR 0.012 0.001 TYR D 43 PHE 0.010 0.001 PHE H 93 TRP 0.005 0.001 TRP I 173 HIS 0.003 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00237 (12782) covalent geometry : angle 0.57267 (17272) hydrogen bonds : bond 0.04349 ( 430) hydrogen bonds : angle 5.15527 ( 1222) metal coordination : bond 0.00428 ( 4) Misc. bond : bond 0.00050 ( 5) *********************** 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 155 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.334 Fit side-chains REVERT: A 119 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8401 (mtm180) REVERT: A 155 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8627 (tp30) REVERT: A 364 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: A 385 SER cc_start: 0.9178 (t) cc_final: 0.8563 (p) REVERT: D 57 LYS cc_start: 0.7818 (tttt) cc_final: 0.7383 (tptt) REVERT: E 119 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8391 (mtm180) REVERT: E 364 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6560 (mm-30) REVERT: E 385 SER cc_start: 0.9141 (t) cc_final: 0.8647 (p) REVERT: I 198 LEU cc_start: 0.8070 (mm) cc_final: 0.7666 (mt) REVERT: J 152 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8054 (mmtt) outliers start: 11 outliers final: 2 residues processed: 150 average time/residue: 0.1558 time to fit residues: 30.9512 Evaluate side-chains 123 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU 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 47 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN D 42 HIS H 42 HIS J 177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107023 restraints weight = 32912.370| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.33 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12791 Z= 0.154 Angle : 0.571 6.568 17272 Z= 0.286 Chirality : 0.045 0.134 1950 Planarity : 0.004 0.053 2216 Dihedral : 8.266 144.452 1800 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.88 % Allowed : 10.78 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.19), residues: 1574 helix: -1.72 (0.18), residues: 704 sheet: -2.27 (0.30), residues: 244 loop : -2.20 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 57 TYR 0.013 0.002 TYR F 28 PHE 0.010 0.001 PHE B 23 TRP 0.006 0.001 TRP I 168 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00375 (12782) covalent geometry : angle 0.57147 (17272) hydrogen bonds : bond 0.04468 ( 430) hydrogen bonds : angle 4.67440 ( 1222) metal coordination : bond 0.00537 ( 4) Misc. bond : bond 0.00037 ( 5) *********************** 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 168 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.348 Fit side-chains REVERT: A 119 ARG cc_start: 0.8309 (mtm180) cc_final: 0.8074 (mtm180) REVERT: A 324 LYS cc_start: 0.7954 (mttm) cc_final: 0.7703 (mtmm) REVERT: B 44 LYS cc_start: 0.8810 (tttt) cc_final: 0.8248 (ttpp) REVERT: C 39 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: D 57 LYS cc_start: 0.7714 (tttt) cc_final: 0.7476 (tptt) REVERT: E 119 ARG cc_start: 0.8303 (mtm180) cc_final: 0.8082 (mtm180) REVERT: E 324 LYS cc_start: 0.7988 (mttm) cc_final: 0.7727 (mtmm) REVERT: E 364 GLU cc_start: 0.7714 (mp0) cc_final: 0.7265 (tm-30) REVERT: E 385 SER cc_start: 0.9048 (t) cc_final: 0.8837 (p) REVERT: G 39 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: J 153 GLN cc_start: 0.8730 (mt0) cc_final: 0.8509 (mt0) outliers start: 12 outliers final: 3 residues processed: 161 average time/residue: 0.1248 time to fit residues: 26.7862 Evaluate side-chains 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.112346 restraints weight = 27778.549| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.50 r_work: 0.2690 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12791 Z= 0.093 Angle : 0.490 5.911 17272 Z= 0.248 Chirality : 0.042 0.127 1950 Planarity : 0.003 0.051 2216 Dihedral : 7.851 151.590 1800 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.73 % Allowed : 11.73 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.20), residues: 1574 helix: -1.17 (0.19), residues: 710 sheet: -1.71 (0.31), residues: 260 loop : -1.96 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 145 TYR 0.009 0.001 TYR F 28 PHE 0.006 0.001 PHE H 93 TRP 0.003 0.001 TRP I 168 HIS 0.003 0.000 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00206 (12782) covalent geometry : angle 0.48990 (17272) hydrogen bonds : bond 0.03288 ( 430) hydrogen bonds : angle 4.25006 ( 1222) metal coordination : bond 0.00074 ( 4) Misc. bond : bond 0.00024 ( 5) *********************** 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 149 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.506 Fit side-chains REVERT: A 119 ARG cc_start: 0.8781 (mtm180) cc_final: 0.8538 (mtm180) REVERT: A 324 LYS cc_start: 0.8266 (mttm) cc_final: 0.7951 (mtmm) REVERT: A 362 GLU cc_start: 0.7414 (tt0) cc_final: 0.7133 (tt0) REVERT: A 364 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6559 (mm-30) REVERT: A 385 SER cc_start: 0.9128 (t) cc_final: 0.8680 (p) REVERT: B 44 LYS cc_start: 0.8770 (tttt) cc_final: 0.8141 (ttpp) REVERT: C 39 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: C 45 MET cc_start: 0.8341 (mtm) cc_final: 0.8087 (mtp) REVERT: D 57 LYS cc_start: 0.7755 (tttt) cc_final: 0.7391 (tptt) REVERT: E 119 ARG cc_start: 0.8785 (mtm180) cc_final: 0.8548 (mtm180) REVERT: E 324 LYS cc_start: 0.8275 (mttm) cc_final: 0.7952 (mtmm) REVERT: E 364 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: E 385 SER cc_start: 0.9136 (t) cc_final: 0.8740 (p) REVERT: F 44 LYS cc_start: 0.8765 (tttm) cc_final: 0.8495 (tttt) REVERT: G 39 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: I 189 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7885 (tt0) outliers start: 10 outliers final: 6 residues processed: 146 average time/residue: 0.1539 time to fit residues: 29.9962 Evaluate side-chains 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 364 GLU 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 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 0.0170 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.144001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110288 restraints weight = 31407.876| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.49 r_work: 0.2633 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12791 Z= 0.083 Angle : 0.464 6.456 17272 Z= 0.235 Chirality : 0.042 0.124 1950 Planarity : 0.003 0.051 2216 Dihedral : 7.657 153.553 1800 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.32 % Allowed : 11.95 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.20), residues: 1574 helix: -0.71 (0.20), residues: 712 sheet: -1.32 (0.32), residues: 260 loop : -1.70 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 328 TYR 0.012 0.001 TYR H 43 PHE 0.006 0.001 PHE F 40 TRP 0.005 0.000 TRP D 108 HIS 0.002 0.000 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00179 (12782) covalent geometry : angle 0.46365 (17272) hydrogen bonds : bond 0.02982 ( 430) hydrogen bonds : angle 4.01387 ( 1222) metal coordination : bond 0.00064 ( 4) Misc. bond : bond 0.00027 ( 5) *********************** 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 154 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.500 Fit side-chains REVERT: A 119 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8589 (mtm180) REVERT: A 324 LYS cc_start: 0.8157 (mttm) cc_final: 0.7838 (mtmm) REVERT: A 347 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7398 (mmmt) REVERT: A 362 GLU cc_start: 0.7424 (tt0) cc_final: 0.6852 (tt0) REVERT: A 364 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: A 385 SER cc_start: 0.9033 (t) cc_final: 0.8609 (p) REVERT: B 44 LYS cc_start: 0.8638 (tttt) cc_final: 0.8044 (ttpp) REVERT: C 39 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: C 45 MET cc_start: 0.8050 (mtm) cc_final: 0.7830 (mtm) REVERT: D 57 LYS cc_start: 0.7719 (tttt) cc_final: 0.7305 (tptt) REVERT: E 119 ARG cc_start: 0.8806 (mtm180) cc_final: 0.8594 (mtm180) REVERT: E 324 LYS cc_start: 0.8161 (mttm) cc_final: 0.7802 (mtmm) REVERT: E 334 MET cc_start: 0.8579 (mtt) cc_final: 0.8306 (mtt) REVERT: E 364 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: E 385 SER cc_start: 0.8967 (t) cc_final: 0.8616 (p) REVERT: F 44 LYS cc_start: 0.8647 (tttm) cc_final: 0.8353 (tttt) REVERT: G 39 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: H 108 TRP cc_start: 0.7770 (m-10) cc_final: 0.7316 (m-10) REVERT: I 118 TYR cc_start: 0.7286 (p90) cc_final: 0.6990 (p90) REVERT: I 189 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7832 (tt0) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.1525 time to fit residues: 30.3429 Evaluate side-chains 145 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 382 THR Chi-restraints excluded: chain B residue 17 LEU 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 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN F 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.104610 restraints weight = 30944.582| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.05 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12791 Z= 0.203 Angle : 0.586 7.493 17272 Z= 0.293 Chirality : 0.047 0.138 1950 Planarity : 0.004 0.054 2216 Dihedral : 8.184 157.448 1800 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.47 % Allowed : 12.46 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.20), residues: 1574 helix: -0.84 (0.19), residues: 718 sheet: -1.32 (0.32), residues: 256 loop : -1.85 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 328 TYR 0.021 0.002 TYR D 43 PHE 0.014 0.002 PHE F 23 TRP 0.007 0.001 TRP I 168 HIS 0.004 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00506 (12782) covalent geometry : angle 0.58639 (17272) hydrogen bonds : bond 0.04443 ( 430) hydrogen bonds : angle 4.44265 ( 1222) metal coordination : bond 0.00270 ( 4) Misc. bond : bond 0.00035 ( 5) *********************** 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 161 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.599 Fit side-chains REVERT: A 119 ARG cc_start: 0.8400 (mtm180) cc_final: 0.8174 (mtm180) REVERT: A 324 LYS cc_start: 0.7925 (mttm) cc_final: 0.7675 (mtmm) REVERT: A 362 GLU cc_start: 0.7357 (tt0) cc_final: 0.7114 (tt0) REVERT: C 39 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: D 57 LYS cc_start: 0.7588 (tttt) cc_final: 0.7362 (tptt) REVERT: E 324 LYS cc_start: 0.7956 (mttm) cc_final: 0.7689 (mtmm) REVERT: E 385 SER cc_start: 0.9206 (t) cc_final: 0.8879 (p) REVERT: F 44 LYS cc_start: 0.8817 (tttm) cc_final: 0.8517 (tttt) REVERT: G 39 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: J 191 THR cc_start: 0.8929 (m) cc_final: 0.8610 (p) outliers start: 20 outliers final: 16 residues processed: 153 average time/residue: 0.1672 time to fit residues: 34.4144 Evaluate side-chains 149 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 17 LEU 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 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 443 VAL 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 122 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.102287 restraints weight = 43079.080| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.99 r_work: 0.2533 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12791 Z= 0.227 Angle : 0.606 8.387 17272 Z= 0.301 Chirality : 0.047 0.141 1950 Planarity : 0.004 0.048 2216 Dihedral : 8.448 161.733 1800 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.20), residues: 1574 helix: -0.79 (0.19), residues: 714 sheet: -1.32 (0.31), residues: 256 loop : -1.90 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 328 TYR 0.021 0.002 TYR D 43 PHE 0.015 0.002 PHE F 23 TRP 0.006 0.001 TRP A 454 HIS 0.004 0.001 HIS E 257 Details of bonding type rmsd covalent geometry : bond 0.00571 (12782) covalent geometry : angle 0.60589 (17272) hydrogen bonds : bond 0.04541 ( 430) hydrogen bonds : angle 4.47581 ( 1222) metal coordination : bond 0.00239 ( 4) Misc. bond : bond 0.00041 ( 5) *********************** 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 161 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.484 Fit side-chains REVERT: A 119 ARG cc_start: 0.8865 (mtm180) cc_final: 0.8659 (mtm-85) REVERT: A 324 LYS cc_start: 0.8039 (mttm) cc_final: 0.7663 (mtmm) REVERT: A 327 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7588 (tt0) REVERT: A 362 GLU cc_start: 0.7826 (tt0) cc_final: 0.7512 (tt0) REVERT: C 39 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: C 61 GLU cc_start: 0.7277 (tt0) cc_final: 0.6950 (tm-30) REVERT: D 57 LYS cc_start: 0.7657 (tttt) cc_final: 0.7187 (tptt) REVERT: E 324 LYS cc_start: 0.8024 (mttm) cc_final: 0.7634 (mtmm) REVERT: E 327 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7628 (tt0) REVERT: F 44 LYS cc_start: 0.8725 (tttm) cc_final: 0.8419 (tttt) REVERT: G 39 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: I 191 THR cc_start: 0.8434 (m) cc_final: 0.8142 (p) REVERT: J 191 THR cc_start: 0.8376 (m) cc_final: 0.7991 (p) outliers start: 24 outliers final: 20 residues processed: 151 average time/residue: 0.1649 time to fit residues: 33.4675 Evaluate side-chains 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 17 LEU 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 66 THR Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 443 VAL 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 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.108525 restraints weight = 36295.237| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.51 r_work: 0.2596 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12791 Z= 0.118 Angle : 0.507 6.972 17272 Z= 0.255 Chirality : 0.043 0.131 1950 Planarity : 0.003 0.043 2216 Dihedral : 8.110 160.269 1800 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.39 % Allowed : 12.90 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.20), residues: 1574 helix: -0.31 (0.20), residues: 708 sheet: -1.14 (0.32), residues: 256 loop : -1.74 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.014 0.001 TYR D 43 PHE 0.008 0.001 PHE F 23 TRP 0.006 0.001 TRP D 108 HIS 0.002 0.001 HIS E 89 Details of bonding type rmsd covalent geometry : bond 0.00282 (12782) covalent geometry : angle 0.50729 (17272) hydrogen bonds : bond 0.03540 ( 430) hydrogen bonds : angle 4.18828 ( 1222) metal coordination : bond 0.00077 ( 4) Misc. bond : bond 0.00016 ( 5) *********************** 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 157 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8868 (mtm180) cc_final: 0.8595 (mtm180) REVERT: A 324 LYS cc_start: 0.8094 (mttm) cc_final: 0.7732 (mtmm) REVERT: A 362 GLU cc_start: 0.7550 (tt0) cc_final: 0.7190 (tt0) REVERT: C 39 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: E 324 LYS cc_start: 0.8104 (mttm) cc_final: 0.7736 (mtmm) REVERT: G 39 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: I 191 THR cc_start: 0.8461 (m) cc_final: 0.8111 (p) REVERT: I 192 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7918 (tttm) REVERT: J 101 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7623 (mt-10) REVERT: J 191 THR cc_start: 0.8298 (m) cc_final: 0.7970 (p) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.1666 time to fit residues: 33.0541 Evaluate side-chains 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 17 LEU 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 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 443 VAL 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 122 ASP Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.138241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.103777 restraints weight = 36897.713| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 5.87 r_work: 0.2541 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12791 Z= 0.135 Angle : 0.518 6.847 17272 Z= 0.259 Chirality : 0.044 0.129 1950 Planarity : 0.003 0.046 2216 Dihedral : 8.127 160.652 1800 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.47 % Allowed : 12.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1574 helix: -0.12 (0.20), residues: 708 sheet: -1.09 (0.32), residues: 256 loop : -1.69 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.015 0.001 TYR D 43 PHE 0.010 0.001 PHE F 23 TRP 0.006 0.001 TRP D 108 HIS 0.002 0.001 HIS E 89 Details of bonding type rmsd covalent geometry : bond 0.00330 (12782) covalent geometry : angle 0.51803 (17272) hydrogen bonds : bond 0.03685 ( 430) hydrogen bonds : angle 4.17980 ( 1222) metal coordination : bond 0.00169 ( 4) Misc. bond : bond 0.00023 ( 5) *********************** 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 155 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8881 (mtm180) cc_final: 0.8615 (mtm180) REVERT: A 324 LYS cc_start: 0.8049 (mttm) cc_final: 0.7701 (mtmm) REVERT: A 362 GLU cc_start: 0.7722 (tt0) cc_final: 0.7351 (tt0) REVERT: C 39 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: C 61 GLU cc_start: 0.7404 (tt0) cc_final: 0.6890 (tm-30) REVERT: E 324 LYS cc_start: 0.8037 (mttm) cc_final: 0.7681 (mtmm) REVERT: E 385 SER cc_start: 0.9152 (t) cc_final: 0.8664 (p) REVERT: G 39 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: I 101 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7657 (mt-10) REVERT: I 191 THR cc_start: 0.8497 (m) cc_final: 0.8115 (p) REVERT: I 192 LYS cc_start: 0.8059 (tmmt) cc_final: 0.7737 (tttm) outliers start: 20 outliers final: 16 residues processed: 146 average time/residue: 0.1585 time to fit residues: 31.3862 Evaluate side-chains 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 17 LEU 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 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 443 VAL 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 122 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.4980 chunk 130 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.141096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108528 restraints weight = 31748.209| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.32 r_work: 0.2619 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12791 Z= 0.089 Angle : 0.474 5.916 17272 Z= 0.239 Chirality : 0.042 0.125 1950 Planarity : 0.003 0.045 2216 Dihedral : 7.927 158.871 1800 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.17 % Allowed : 13.05 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.21), residues: 1574 helix: 0.22 (0.21), residues: 708 sheet: -1.09 (0.32), residues: 266 loop : -1.54 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.012 0.001 TYR D 43 PHE 0.006 0.001 PHE F 23 TRP 0.008 0.001 TRP D 108 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00197 (12782) covalent geometry : angle 0.47384 (17272) hydrogen bonds : bond 0.03073 ( 430) hydrogen bonds : angle 3.98869 ( 1222) metal coordination : bond 0.00087 ( 4) Misc. bond : bond 0.00021 ( 5) ********************** 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 150 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.531 Fit side-chains REVERT: A 119 ARG cc_start: 0.8817 (mtm180) cc_final: 0.8550 (mtm180) REVERT: A 324 LYS cc_start: 0.8083 (mttm) cc_final: 0.7758 (mtmm) REVERT: A 347 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7428 (mmmt) REVERT: A 362 GLU cc_start: 0.7453 (tt0) cc_final: 0.7043 (tt0) REVERT: A 364 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6582 (mm-30) REVERT: C 39 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: D 57 LYS cc_start: 0.7472 (tttt) cc_final: 0.7085 (ttpp) REVERT: E 324 LYS cc_start: 0.8075 (mttm) cc_final: 0.7744 (mtmm) REVERT: E 385 SER cc_start: 0.9116 (t) cc_final: 0.8681 (p) REVERT: G 39 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: I 191 THR cc_start: 0.8443 (m) cc_final: 0.8078 (p) REVERT: I 192 LYS cc_start: 0.8067 (tmmt) cc_final: 0.7743 (tttm) REVERT: J 101 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7626 (mt-10) REVERT: J 191 THR cc_start: 0.8302 (m) cc_final: 0.7985 (p) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.1640 time to fit residues: 31.3267 Evaluate side-chains 147 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 382 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 12 optimal weight: 0.0270 chunk 23 optimal weight: 0.0040 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110938 restraints weight = 33325.393| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 4.82 r_work: 0.2636 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12791 Z= 0.077 Angle : 0.452 5.403 17272 Z= 0.229 Chirality : 0.042 0.124 1950 Planarity : 0.003 0.046 2216 Dihedral : 7.703 156.201 1800 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.88 % Allowed : 13.56 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1574 helix: 0.54 (0.21), residues: 706 sheet: -0.96 (0.32), residues: 266 loop : -1.39 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 328 TYR 0.021 0.001 TYR D 43 PHE 0.007 0.001 PHE F 40 TRP 0.007 0.001 TRP D 108 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00160 (12782) covalent geometry : angle 0.45230 (17272) hydrogen bonds : bond 0.02652 ( 430) hydrogen bonds : angle 3.81482 ( 1222) metal coordination : bond 0.00054 ( 4) Misc. bond : bond 0.00026 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.48 seconds wall clock time: 51 minutes 52.65 seconds (3112.65 seconds total)